diff --git a/latest/examples/gwas_tutorial.html b/latest/examples/gwas_tutorial.html
index eca6dfb2b..6a2135615 100644
--- a/latest/examples/gwas_tutorial.html
+++ b/latest/examples/gwas_tutorial.html
@@ -618,7 +618,7 @@ <h2>Importing data from VCF<a class="headerlink" href="#importing-data-from-vcf"
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>    Scan:   0%|          | 0.00/1.00 [00:00&lt;?, ?files/s]
     Scan:   0%|          | 0.00/1.00 [00:00&lt;?, ?files/s]
     Scan:   0%|          | 0.00/1.00 [00:00&lt;?, ?files/s]
-    Scan: 100%|██████████| 1.00/1.00 [00:00&lt;00:00, 1.57files/s]
+    Scan: 100%|██████████| 1.00/1.00 [00:00&lt;00:00, 1.59files/s]
 </pre></div>
 </div>
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> Explode:   0%|          | 0.00/10.9k [00:00&lt;?, ?vars/s]
@@ -629,83 +629,83 @@ <h2>Importing data from VCF<a class="headerlink" href="#importing-data-from-vcf"
 </div>
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> Explode:   0%|          | 0.00/10.9k [00:00&lt;?, ?vars/s]
  Explode:   0%|          | 0.00/10.9k [00:00&lt;?, ?vars/s]
- Explode:   0%|          | 50.0/10.9k [00:00&lt;00:21, 495vars/s]
- Explode:   2%|▏         | 263/10.9k [00:00&lt;00:07, 1.34kvars/s]
- Explode:   4%|▍         | 477/10.9k [00:00&lt;00:06, 1.63kvars/s]
- Explode:   6%|▋         | 691/10.9k [00:00&lt;00:05, 1.77kvars/s]
- Explode:   8%|▊         | 903/10.9k [00:01&lt;00:05, 1.85kvars/s]
- Explode:   9%|▉         | 1.02k/10.9k [00:02&lt;00:17, 559vars/s]
- Explode:  11%|█▏        | 1.24k/10.9k [00:02&lt;00:14, 674vars/s]
- Explode:  13%|█▎        | 1.46k/10.9k [00:02&lt;00:12, 783vars/s]
- Explode:  15%|█▌        | 1.67k/10.9k [00:02&lt;00:10, 885vars/s]
- Explode:  17%|█▋        | 1.82k/10.9k [00:03&lt;00:16, 546vars/s]
- Explode:  19%|█▊        | 2.03k/10.9k [00:03&lt;00:14, 623vars/s]
- Explode:  21%|██        | 2.25k/10.9k [00:03&lt;00:12, 698vars/s]
- Explode:  23%|██▎       | 2.46k/10.9k [00:03&lt;00:10, 776vars/s]
- Explode:  24%|██▍       | 2.64k/10.9k [00:04&lt;00:14, 561vars/s]
- Explode:  26%|██▌       | 2.78k/10.9k [00:05&lt;00:15, 511vars/s]
- Explode:  28%|██▊       | 3.00k/10.9k [00:05&lt;00:13, 573vars/s]
- Explode:  29%|██▉       | 3.15k/10.9k [00:05&lt;00:15, 496vars/s]
- Explode:  31%|███       | 3.37k/10.9k [00:06&lt;00:13, 555vars/s]
- Explode:  33%|███▎      | 3.59k/10.9k [00:06&lt;00:11, 615vars/s]
- Explode:  35%|███▍      | 3.78k/10.9k [00:06&lt;00:10, 666vars/s]
- Explode:  36%|███▌      | 3.93k/10.9k [00:07&lt;00:13, 527vars/s]
- Explode:  38%|███▊      | 4.16k/10.9k [00:07&lt;00:11, 584vars/s]
- Explode:  40%|████      | 4.38k/10.9k [00:07&lt;00:10, 642vars/s]
- Explode:  42%|████▏     | 4.53k/10.9k [00:08&lt;00:12, 521vars/s]
- Explode:  44%|████▎     | 4.76k/10.9k [00:08&lt;00:10, 576vars/s]
- Explode:  46%|████▌     | 4.98k/10.9k [00:08&lt;00:09, 632vars/s]
- Explode:  47%|████▋     | 5.14k/10.9k [00:09&lt;00:10, 532vars/s]
- Explode:  49%|████▉     | 5.37k/10.9k [00:09&lt;00:09, 586vars/s]
- Explode:  51%|█████     | 5.52k/10.9k [00:10&lt;00:11, 472vars/s]
- Explode:  53%|█████▎    | 5.75k/10.9k [00:10&lt;00:09, 521vars/s]
- Explode:  54%|█████▍    | 5.92k/10.9k [00:10&lt;00:08, 557vars/s]
- Explode:  56%|█████▌    | 6.08k/10.9k [00:11&lt;00:09, 500vars/s]
- Explode:  58%|█████▊    | 6.30k/10.9k [00:11&lt;00:08, 551vars/s]
- Explode:  59%|█████▉    | 6.45k/10.9k [00:11&lt;00:07, 581vars/s]
- Explode:  61%|██████    | 6.60k/10.9k [00:12&lt;00:08, 495vars/s]
- Explode:  62%|██████▏   | 6.78k/10.9k [00:12&lt;00:07, 534vars/s]
- Explode:  64%|██████▍   | 6.99k/10.9k [00:12&lt;00:06, 581vars/s]
- Explode:  66%|██████▌   | 7.13k/10.9k [00:13&lt;00:07, 490vars/s]
- Explode:  68%|██████▊   | 7.35k/10.9k [00:13&lt;00:06, 541vars/s]
- Explode:  70%|██████▉   | 7.57k/10.9k [00:13&lt;00:05, 593vars/s]
- Explode:  71%|███████   | 7.74k/10.9k [00:14&lt;00:06, 508vars/s]
- Explode:  73%|███████▎  | 7.92k/10.9k [00:14&lt;00:05, 547vars/s]
- Explode:  74%|███████▍  | 8.07k/10.9k [00:14&lt;00:05, 497vars/s]
- Explode:  75%|███████▌  | 8.21k/10.9k [00:15&lt;00:05, 466vars/s]
- Explode:  77%|███████▋  | 8.33k/10.9k [00:15&lt;00:05, 443vars/s]
- Explode:  79%|███████▊  | 8.55k/10.9k [00:16&lt;00:04, 493vars/s]
- Explode:  80%|███████▉  | 8.68k/10.9k [00:16&lt;00:04, 448vars/s]
- Explode:  82%|████████▏ | 8.90k/10.9k [00:16&lt;00:03, 498vars/s]
- Explode:  83%|████████▎ | 9.03k/10.9k [00:17&lt;00:04, 450vars/s]
- Explode:  85%|████████▌ | 9.26k/10.9k [00:17&lt;00:03, 501vars/s]
- Explode:  86%|████████▋ | 9.39k/10.9k [00:18&lt;00:03, 455vars/s]
- Explode:  88%|████████▊ | 9.62k/10.9k [00:18&lt;00:02, 505vars/s]
- Explode:  90%|████████▉ | 9.76k/10.9k [00:18&lt;00:02, 467vars/s]
- Explode:  92%|█████████▏| 9.97k/10.9k [00:18&lt;00:01, 514vars/s]
- Explode:  93%|█████████▎| 10.1k/10.9k [00:19&lt;00:01, 468vars/s]
- Explode:  95%|█████████▍| 10.3k/10.9k [00:19&lt;00:01, 507vars/s]
- Explode:  96%|█████████▌| 10.4k/10.9k [00:20&lt;00:01, 465vars/s]
- Explode:  97%|█████████▋| 10.5k/10.9k [00:20&lt;00:00, 438vars/s]
- Explode:  98%|█████████▊| 10.6k/10.9k [00:21&lt;00:00, 414vars/s]
- Explode: 100%|█████████▉| 10.9k/10.9k [00:21&lt;00:00, 465vars/s]
- Explode: 100%|██████████| 10.9k/10.9k [00:21&lt;00:00, 510vars/s]
+ Explode:   1%|          | 66.0/10.9k [00:00&lt;00:16, 654vars/s]
+ Explode:   3%|▎         | 281/10.9k [00:00&lt;00:07, 1.43kvars/s]
+ Explode:   5%|▍         | 495/10.9k [00:00&lt;00:06, 1.68kvars/s]
+ Explode:   7%|▋         | 709/10.9k [00:00&lt;00:05, 1.81kvars/s]
+ Explode:   8%|▊         | 909/10.9k [00:01&lt;00:05, 1.85kvars/s]
+ Explode:   9%|▉         | 1.03k/10.9k [00:02&lt;00:17, 576vars/s]
+ Explode:  11%|█▏        | 1.25k/10.9k [00:02&lt;00:13, 696vars/s]
+ Explode:  14%|█▎        | 1.47k/10.9k [00:02&lt;00:11, 810vars/s]
+ Explode:  16%|█▌        | 1.69k/10.9k [00:02&lt;00:10, 918vars/s]
+ Explode:  17%|█▋        | 1.84k/10.9k [00:03&lt;00:15, 570vars/s]
+ Explode:  19%|█▉        | 2.07k/10.9k [00:03&lt;00:13, 650vars/s]
+ Explode:  21%|██        | 2.29k/10.9k [00:03&lt;00:11, 730vars/s]
+ Explode:  23%|██▎       | 2.49k/10.9k [00:03&lt;00:10, 801vars/s]
+ Explode:  24%|██▍       | 2.65k/10.9k [00:04&lt;00:14, 578vars/s]
+ Explode:  26%|██▌       | 2.80k/10.9k [00:05&lt;00:15, 529vars/s]
+ Explode:  28%|██▊       | 3.02k/10.9k [00:05&lt;00:13, 595vars/s]
+ Explode:  29%|██▉       | 3.17k/10.9k [00:05&lt;00:14, 514vars/s]
+ Explode:  31%|███       | 3.39k/10.9k [00:05&lt;00:13, 575vars/s]
+ Explode:  33%|███▎      | 3.61k/10.9k [00:05&lt;00:11, 638vars/s]
+ Explode:  35%|███▍      | 3.78k/10.9k [00:06&lt;00:10, 680vars/s]
+ Explode:  36%|███▋      | 3.94k/10.9k [00:06&lt;00:12, 544vars/s]
+ Explode:  38%|███▊      | 4.17k/10.9k [00:07&lt;00:11, 603vars/s]
+ Explode:  40%|████      | 4.39k/10.9k [00:07&lt;00:09, 663vars/s]
+ Explode:  42%|████▏     | 4.54k/10.9k [00:08&lt;00:11, 535vars/s]
+ Explode:  44%|████▍     | 4.77k/10.9k [00:08&lt;00:10, 591vars/s]
+ Explode:  46%|████▌     | 4.99k/10.9k [00:08&lt;00:09, 649vars/s]
+ Explode:  47%|████▋     | 5.16k/10.9k [00:08&lt;00:10, 546vars/s]
+ Explode:  49%|████▉     | 5.38k/10.9k [00:09&lt;00:09, 600vars/s]
+ Explode:  51%|█████     | 5.53k/10.9k [00:10&lt;00:11, 480vars/s]
+ Explode:  53%|█████▎    | 5.75k/10.9k [00:10&lt;00:09, 530vars/s]
+ Explode:  54%|█████▍    | 5.92k/10.9k [00:10&lt;00:08, 565vars/s]
+ Explode:  56%|█████▌    | 6.07k/10.9k [00:10&lt;00:09, 506vars/s]
+ Explode:  58%|█████▊    | 6.29k/10.9k [00:11&lt;00:08, 556vars/s]
+ Explode:  59%|█████▉    | 6.45k/10.9k [00:11&lt;00:07, 592vars/s]
+ Explode:  61%|██████    | 6.61k/10.9k [00:11&lt;00:08, 511vars/s]
+ Explode:  63%|██████▎   | 6.81k/10.9k [00:11&lt;00:07, 556vars/s]
+ Explode:  65%|██████▍   | 7.02k/10.9k [00:12&lt;00:06, 606vars/s]
+ Explode:  66%|██████▌   | 7.17k/10.9k [00:12&lt;00:07, 513vars/s]
+ Explode:  68%|██████▊   | 7.39k/10.9k [00:12&lt;00:06, 565vars/s]
+ Explode:  70%|██████▉   | 7.59k/10.9k [00:13&lt;00:05, 612vars/s]
+ Explode:  71%|███████   | 7.74k/10.9k [00:13&lt;00:06, 519vars/s]
+ Explode:  73%|███████▎  | 7.92k/10.9k [00:13&lt;00:05, 560vars/s]
+ Explode:  74%|███████▍  | 8.08k/10.9k [00:14&lt;00:05, 511vars/s]
+ Explode:  76%|███████▌  | 8.23k/10.9k [00:15&lt;00:05, 477vars/s]
+ Explode:  77%|███████▋  | 8.36k/10.9k [00:15&lt;00:05, 456vars/s]
+ Explode:  79%|███████▉  | 8.59k/10.9k [00:15&lt;00:04, 507vars/s]
+ Explode:  80%|████████  | 8.72k/10.9k [00:16&lt;00:04, 463vars/s]
+ Explode:  82%|████████▏ | 8.95k/10.9k [00:16&lt;00:03, 514vars/s]
+ Explode:  83%|████████▎ | 9.07k/10.9k [00:16&lt;00:03, 465vars/s]
+ Explode:  85%|████████▌ | 9.30k/10.9k [00:17&lt;00:03, 516vars/s]
+ Explode:  87%|████████▋ | 9.43k/10.9k [00:17&lt;00:03, 470vars/s]
+ Explode:  89%|████████▊ | 9.63k/10.9k [00:17&lt;00:02, 514vars/s]
+ Explode:  90%|████████▉ | 9.75k/10.9k [00:18&lt;00:02, 472vars/s]
+ Explode:  92%|█████████▏| 9.97k/10.9k [00:18&lt;00:01, 523vars/s]
+ Explode:  93%|█████████▎| 10.1k/10.9k [00:18&lt;00:01, 478vars/s]
+ Explode:  95%|█████████▍| 10.3k/10.9k [00:19&lt;00:01, 514vars/s]
+ Explode:  96%|█████████▌| 10.4k/10.9k [00:19&lt;00:01, 469vars/s]
+ Explode:  97%|█████████▋| 10.5k/10.9k [00:20&lt;00:00, 445vars/s]
+ Explode:  98%|█████████▊| 10.6k/10.9k [00:20&lt;00:00, 420vars/s]
+ Explode: 100%|█████████▉| 10.9k/10.9k [00:20&lt;00:00, 472vars/s]
+ Explode: 100%|██████████| 10.9k/10.9k [00:20&lt;00:00, 522vars/s]
 </pre></div>
 </div>
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>  Encode:   0%|          | 0.00/28.2M [00:00&lt;?, ?B/s]
   Encode:   0%|          | 0.00/28.2M [00:00&lt;?, ?B/s]
   Encode:   0%|          | 0.00/28.2M [00:00&lt;?, ?B/s]
   Encode:   0%|          | 0.00/28.2M [00:00&lt;?, ?B/s]
-  Encode:   0%|          | 90.0k/28.2M [00:00&lt;00:31, 889kB/s]
-  Encode:   1%|          | 270k/28.2M [00:00&lt;00:22, 1.23MB/s]
-  Encode:   1%|          | 350k/28.2M [00:00&lt;00:25, 1.08MB/s]
-  Encode:  21%|██▏       | 6.03M/28.2M [00:01&lt;00:02, 7.86MB/s]
-  Encode:  31%|███▏      | 8.87M/28.2M [00:01&lt;00:02, 9.38MB/s]
-  Encode:  42%|████▏     | 11.7M/28.2M [00:01&lt;00:01, 10.3MB/s]
-  Encode:  62%|██████▏   | 17.4M/28.2M [00:01&lt;00:00, 11.8MB/s]
-  Encode:  92%|█████████▏| 25.9M/28.2M [00:01&lt;00:00, 17.7MB/s]
-  Encode: 100%|██████████| 28.2M/28.2M [00:02&lt;00:00, 15.7MB/s]
-  Encode: 100%|██████████| 28.2M/28.2M [00:02&lt;00:00, 12.4MB/s]
+  Encode:   0%|          | 90.0k/28.2M [00:00&lt;00:31, 891kB/s]
+  Encode:   1%|          | 270k/28.2M [00:00&lt;00:21, 1.29MB/s]
+  Encode:   1%|          | 350k/28.2M [00:00&lt;00:25, 1.11MB/s]
+  Encode:  21%|██▏       | 6.03M/28.2M [00:01&lt;00:02, 8.30MB/s]
+  Encode:  31%|███▏      | 8.87M/28.2M [00:01&lt;00:01, 9.79MB/s]
+  Encode:  42%|████▏     | 11.7M/28.2M [00:01&lt;00:01, 10.9MB/s]
+  Encode:  62%|██████▏   | 17.4M/28.2M [00:01&lt;00:00, 12.3MB/s]
+  Encode:  92%|█████████▏| 25.9M/28.2M [00:01&lt;00:00, 18.5MB/s]
+  Encode: 100%|██████████| 28.2M/28.2M [00:02&lt;00:00, 16.4MB/s]
+  Encode: 100%|██████████| 28.2M/28.2M [00:02&lt;00:00, 12.9MB/s]
 </pre></div>
 </div>
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Finalise:   0%|          | 0.00/13.0 [00:00&lt;?, ?array/s]
@@ -1125,7 +1125,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
     variant_id_mask       (variants) bool 11kB dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;
     variant_position      (variants) int32 44kB dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;
     variant_quality       (variants) float32 44kB dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-11874ae4-1604-47b8-8367-344abc760947' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-11874ae4-1604-47b8-8367-344abc760947' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>samples</span>: 284</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-55d14494-ba11-4644-89f2-0d49a1663f88' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-55d14494-ba11-4644-89f2-0d49a1663f88' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-9fc34c53-fff8-4f3a-a091-24e91cfd5861' class='xr-section-summary-in' type='checkbox'  checked><label for='section-9fc34c53-fff8-4f3a-a091-24e91cfd5861' class='xr-section-summary' >Data variables: <span>(17)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-71cbec44-a617-4fe4-9e74-aa3d2c72a7f7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-71cbec44-a617-4fe4-9e74-aa3d2c72a7f7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-079fd12d-abb7-45a5-aef1-8c1618c594c5' class='xr-var-data-in' type='checkbox'><label for='data-079fd12d-abb7-45a5-aef1-8c1618c594c5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-9f4d9da9-2ace-4a2f-9d7b-198a5dcd17b1' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-9f4d9da9-2ace-4a2f-9d7b-198a5dcd17b1' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>samples</span>: 284</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-d6e167be-8cec-47bd-966f-8c8475797aaf' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-d6e167be-8cec-47bd-966f-8c8475797aaf' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-f6b3c6b8-5bfa-4664-883a-81c7cf226434' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f6b3c6b8-5bfa-4664-883a-81c7cf226434' class='xr-section-summary' >Data variables: <span>(17)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-c3c77f44-3241-459f-a39a-664581eb705c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c3c77f44-3241-459f-a39a-664581eb705c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-51eee89f-9666-4ecc-9c69-b24d0d46febd' class='xr-var-data-in' type='checkbox'><label for='data-51eee89f-9666-4ecc-9c69-b24d0d46febd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1205,7 +1205,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-2fb54bec-a5a8-4306-b81f-eb150bdd090f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2fb54bec-a5a8-4306-b81f-eb150bdd090f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e8b02b42-5b19-4afc-8a16-23850c841426' class='xr-var-data-in' type='checkbox'><label for='data-e8b02b42-5b19-4afc-8a16-23850c841426' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-9a5deb49-38ab-412c-a31f-cf0dd8c7e48f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9a5deb49-38ab-412c-a31f-cf0dd8c7e48f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b68af545-6cef-4cef-9b89-88323e385aa1' class='xr-var-data-in' type='checkbox'><label for='data-b68af545-6cef-4cef-9b89-88323e385aa1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1261,7 +1261,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-0ef59142-9fe8-4046-be58-042ca7b3f75f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0ef59142-9fe8-4046-be58-042ca7b3f75f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-418c4eaf-1bdf-4c64-8269-bcdd434156ba' class='xr-var-data-in' type='checkbox'><label for='data-418c4eaf-1bdf-4c64-8269-bcdd434156ba' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-ccfd9f81-78a5-45fc-be83-83387584a6e5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ccfd9f81-78a5-45fc-be83-83387584a6e5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2643cf7a-a0a1-4a25-836e-dea1bedbc6e7' class='xr-var-data-in' type='checkbox'><label for='data-2643cf7a-a0a1-4a25-836e-dea1bedbc6e7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1317,7 +1317,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-6f720188-4d16-47b5-89aa-8105edd18f1f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6f720188-4d16-47b5-89aa-8105edd18f1f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-95a28d34-7e6d-4bf2-a1aa-ea156a5e3835' class='xr-var-data-in' type='checkbox'><label for='data-95a28d34-7e6d-4bf2-a1aa-ea156a5e3835' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-2d8447a9-1016-4b7c-8063-f1fefde5b816' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2d8447a9-1016-4b7c-8063-f1fefde5b816' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-098ede4e-8fa4-4751-b5cf-6a78371726a5' class='xr-var-data-in' type='checkbox'><label for='data-098ede4e-8fa4-4751-b5cf-6a78371726a5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1397,7 +1397,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-c1ec9d89-9ee4-4c2a-b1d4-14595f688679' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c1ec9d89-9ee4-4c2a-b1d4-14595f688679' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-04edd01c-ab1a-4174-a01d-dc87f3512903' class='xr-var-data-in' type='checkbox'><label for='data-04edd01c-ab1a-4174-a01d-dc87f3512903' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-d1a8e3a8-8f1f-4fc5-b7ec-b13e94dfff17' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d1a8e3a8-8f1f-4fc5-b7ec-b13e94dfff17' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-87278d75-a968-4ab4-8243-26c991e0c698' class='xr-var-data-in' type='checkbox'><label for='data-87278d75-a968-4ab4-8243-26c991e0c698' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1477,7 +1477,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-957a50b3-3694-48cf-bdce-11c3d3ad7a85' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-957a50b3-3694-48cf-bdce-11c3d3ad7a85' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9b5999bd-8771-48ce-ae6a-2bac625426bd' class='xr-var-data-in' type='checkbox'><label for='data-9b5999bd-8771-48ce-ae6a-2bac625426bd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-82d974a8-53db-48aa-a0d0-21d0d3d36a61' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-82d974a8-53db-48aa-a0d0-21d0d3d36a61' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d95ffe00-3a8f-4335-9dd0-906eeb701f4f' class='xr-var-data-in' type='checkbox'><label for='data-d95ffe00-3a8f-4335-9dd0-906eeb701f4f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1533,7 +1533,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-10d40d3d-8634-4dd6-83a3-a8e00a70efdc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-10d40d3d-8634-4dd6-83a3-a8e00a70efdc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-54f9e59b-a8c0-477f-9c13-e88b730a6e64' class='xr-var-data-in' type='checkbox'><label for='data-54f9e59b-a8c0-477f-9c13-e88b730a6e64' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-b401cf97-031b-456c-ac30-a942b60acdef' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b401cf97-031b-456c-ac30-a942b60acdef' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-48f779ec-1ee8-4acf-aff5-76a09a4bd230' class='xr-var-data-in' type='checkbox'><label for='data-48f779ec-1ee8-4acf-aff5-76a09a4bd230' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1588,7 +1588,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-b54f7228-f73b-49c2-a0e6-08ccb50ca7f0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b54f7228-f73b-49c2-a0e6-08ccb50ca7f0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d6b47565-9458-4b54-a538-f01742ec6b10' class='xr-var-data-in' type='checkbox'><label for='data-d6b47565-9458-4b54-a538-f01742ec6b10' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-525dc449-2096-491d-a273-d5e194052bc2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-525dc449-2096-491d-a273-d5e194052bc2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3aab1e99-f039-4524-94f9-a367e1e8c1b6' class='xr-var-data-in' type='checkbox'><label for='data-3aab1e99-f039-4524-94f9-a367e1e8c1b6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1643,7 +1643,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-69fe7a65-4a48-4d8c-a3ab-d3757f724616' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-69fe7a65-4a48-4d8c-a3ab-d3757f724616' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bb31d3cf-7e39-4d30-85db-134d77a5fb63' class='xr-var-data-in' type='checkbox'><label for='data-bb31d3cf-7e39-4d30-85db-134d77a5fb63' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-63c7514a-c0d1-4b87-96e6-10464bb36956' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-63c7514a-c0d1-4b87-96e6-10464bb36956' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-89bbccb0-3dee-4c89-b6c8-ef7c45acf1cb' class='xr-var-data-in' type='checkbox'><label for='data-89bbccb0-3dee-4c89-b6c8-ef7c45acf1cb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1698,7 +1698,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-67e6fc37-fe10-445f-a8f2-c7d5ade40f8a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-67e6fc37-fe10-445f-a8f2-c7d5ade40f8a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9efc0175-90cf-429d-8b1a-8543214cf583' class='xr-var-data-in' type='checkbox'><label for='data-9efc0175-90cf-429d-8b1a-8543214cf583' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-f5db4cbb-c744-4108-a00f-47080faa124c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f5db4cbb-c744-4108-a00f-47080faa124c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8faf1f12-11c6-4e43-99df-fbaeef69fd0d' class='xr-var-data-in' type='checkbox'><label for='data-8faf1f12-11c6-4e43-99df-fbaeef69fd0d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1753,7 +1753,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-31e0ab7d-8dc6-45bd-bf6e-29c5632d6bea' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-31e0ab7d-8dc6-45bd-bf6e-29c5632d6bea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-605ec9e4-d774-4f2b-a571-75d48633692b' class='xr-var-data-in' type='checkbox'><label for='data-605ec9e4-d774-4f2b-a571-75d48633692b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-b9fb245b-2bb1-4e96-8650-820988de1cf3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b9fb245b-2bb1-4e96-8650-820988de1cf3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-280d179f-cb14-4baf-92f6-26e9bfa3537f' class='xr-var-data-in' type='checkbox'><label for='data-280d179f-cb14-4baf-92f6-26e9bfa3537f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1809,7 +1809,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ed4b2001-ef58-4631-bb93-0fca2791a75f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ed4b2001-ef58-4631-bb93-0fca2791a75f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9e8e5a9f-e7fd-49ba-9534-cf12fb7230fe' class='xr-var-data-in' type='checkbox'><label for='data-9e8e5a9f-e7fd-49ba-9534-cf12fb7230fe' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-de3c8942-033d-4666-b633-f898836db337' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-de3c8942-033d-4666-b633-f898836db337' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c4dd1fe-11aa-4f18-a652-5c61356b7f08' class='xr-var-data-in' type='checkbox'><label for='data-5c4dd1fe-11aa-4f18-a652-5c61356b7f08' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1865,7 +1865,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-3c2ee51c-0a7f-4503-9045-99fbc9d16121' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3c2ee51c-0a7f-4503-9045-99fbc9d16121' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-01708634-7120-4102-9089-c9c5107b43cd' class='xr-var-data-in' type='checkbox'><label for='data-01708634-7120-4102-9089-c9c5107b43cd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-d44a160c-fc59-4414-979d-90d38b4b7f74' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d44a160c-fc59-4414-979d-90d38b4b7f74' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1bbe12c0-d2f7-4933-8c74-94ad4fd91710' class='xr-var-data-in' type='checkbox'><label for='data-1bbe12c0-d2f7-4933-8c74-94ad4fd91710' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1921,7 +1921,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-9f265537-cd4d-451e-a1d7-e5007bd43a29' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9f265537-cd4d-451e-a1d7-e5007bd43a29' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-611fb73d-92fb-49be-b86e-08b3638ad786' class='xr-var-data-in' type='checkbox'><label for='data-611fb73d-92fb-49be-b86e-08b3638ad786' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-cf55897b-0cc7-4668-97fa-0d77f970974b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cf55897b-0cc7-4668-97fa-0d77f970974b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-671ca243-cc2a-40f9-9cee-ee5d1c860056' class='xr-var-data-in' type='checkbox'><label for='data-671ca243-cc2a-40f9-9cee-ee5d1c860056' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1977,7 +1977,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-45f1968c-58a2-4ee6-926a-16286086f5bd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-45f1968c-58a2-4ee6-926a-16286086f5bd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8f216ece-d212-4d8e-95a8-5acc29c74493' class='xr-var-data-in' type='checkbox'><label for='data-8f216ece-d212-4d8e-95a8-5acc29c74493' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-c17976f9-2a52-420b-b3e1-7de54829ffe7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c17976f9-2a52-420b-b3e1-7de54829ffe7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-560790ae-e5be-42fa-b2eb-28d620db3b32' class='xr-var-data-in' type='checkbox'><label for='data-560790ae-e5be-42fa-b2eb-28d620db3b32' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -2033,7 +2033,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-17a2750f-1611-4d21-90c5-d6a5cba9417e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-17a2750f-1611-4d21-90c5-d6a5cba9417e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-afff5ba8-fd3c-458e-aa81-f8e9937bdb79' class='xr-var-data-in' type='checkbox'><label for='data-afff5ba8-fd3c-458e-aa81-f8e9937bdb79' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-98397444-83e3-4276-8149-72768517d38d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-98397444-83e3-4276-8149-72768517d38d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0dc26046-8a7f-41cf-a16d-83888372f2c1' class='xr-var-data-in' type='checkbox'><label for='data-0dc26046-8a7f-41cf-a16d-83888372f2c1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -2089,7 +2089,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-864355d8-79a0-4223-9083-7d735686b9fe' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-864355d8-79a0-4223-9083-7d735686b9fe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4c8fb74f-9fe5-4360-b2d7-1632c02b26d2' class='xr-var-data-in' type='checkbox'><label for='data-4c8fb74f-9fe5-4360-b2d7-1632c02b26d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-4b6290f1-b4d4-4a16-837b-b591e2d7051c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4b6290f1-b4d4-4a16-837b-b591e2d7051c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cc752ce7-33e5-4091-af2d-aaee7364a643' class='xr-var-data-in' type='checkbox'><label for='data-cc752ce7-33e5-4091-af2d-aaee7364a643' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -2145,7 +2145,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-c3e57670-8d36-45b6-b152-0caa048aca42' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c3e57670-8d36-45b6-b152-0caa048aca42' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-8624f57a-d8f2-4c26-a1ce-2163d2ca2381' class='xr-section-summary-in' type='checkbox'  ><label for='section-8624f57a-d8f2-4c26-a1ce-2163d2ca2381' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-a6e1c14f-dd56-410a-a701-496b3520f4ae' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a6e1c14f-dd56-410a-a701-496b3520f4ae' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-1265eb77-0ab8-42b0-9585-6bb922207791' class='xr-section-summary-in' type='checkbox'  ><label for='section-1265eb77-0ab8-42b0-9585-6bb922207791' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -3049,7 +3049,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
     isFemale              (samples) bool 284B False True False ... False True
     PurpleHair            (samples) bool 284B False False False ... True True
     CaffeineConsumption   (samples) int64 2kB 4 4 4 3 6 2 4 2 ... 6 4 6 4 6 5 5
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-56e3f4dd-412f-4452-b7ff-437955a945c6' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-56e3f4dd-412f-4452-b7ff-437955a945c6' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-c8fb0adc-ff25-45b2-9cd0-21c6807b8fb9' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c8fb0adc-ff25-45b2-9cd0-21c6807b8fb9' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-903607a0-bc92-4b24-b508-f07d0780e7b9' class='xr-section-summary-in' type='checkbox'  checked><label for='section-903607a0-bc92-4b24-b508-f07d0780e7b9' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-afa433db-3990-4800-92bc-e80f22960436' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-afa433db-3990-4800-92bc-e80f22960436' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7aa9fdc9-36d5-4140-8fc4-bb6e964cea28' class='xr-var-data-in' type='checkbox'><label for='data-7aa9fdc9-36d5-4140-8fc4-bb6e964cea28' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-35f812db-fc5a-4096-b550-76adf4f06b62' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-35f812db-fc5a-4096-b550-76adf4f06b62' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-2d365e9d-9c58-4c78-996b-798bcbacf6e0' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2d365e9d-9c58-4c78-996b-798bcbacf6e0' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-f978d249-181f-410f-ba80-38b627fbccf8' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f978d249-181f-410f-ba80-38b627fbccf8' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-05bce572-0cea-4cf0-912f-09aac058b597' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-05bce572-0cea-4cf0-912f-09aac058b597' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ae440e66-ca83-4b00-89a9-db7d780dd4ce' class='xr-var-data-in' type='checkbox'><label for='data-ae440e66-ca83-4b00-89a9-db7d780dd4ce' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3129,7 +3129,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-a325c077-a44a-4bd5-99f0-307d78d5a3b5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a325c077-a44a-4bd5-99f0-307d78d5a3b5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a279d45c-82b6-42bf-8b9c-b51b02f84c3f' class='xr-var-data-in' type='checkbox'><label for='data-a279d45c-82b6-42bf-8b9c-b51b02f84c3f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-0f21c038-fc71-4c03-9e81-74fe478e04f6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0f21c038-fc71-4c03-9e81-74fe478e04f6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0b69133c-c3b9-4c3a-b5ee-e5e8f20921a5' class='xr-var-data-in' type='checkbox'><label for='data-0b69133c-c3b9-4c3a-b5ee-e5e8f20921a5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3185,7 +3185,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-449f60f4-8d68-4914-b5fb-6b09cfc054c0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-449f60f4-8d68-4914-b5fb-6b09cfc054c0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1c7a517b-e8a3-4be7-adf2-e2c7aaf07ebb' class='xr-var-data-in' type='checkbox'><label for='data-1c7a517b-e8a3-4be7-adf2-e2c7aaf07ebb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-2eead1f4-07da-44d9-b863-7132ad40041b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2eead1f4-07da-44d9-b863-7132ad40041b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-050096e3-871b-4723-b19c-dee745cd630f' class='xr-var-data-in' type='checkbox'><label for='data-050096e3-871b-4723-b19c-dee745cd630f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3241,7 +3241,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-35ab8c9f-8cbd-4e82-9be5-a56bbf779fae' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-35ab8c9f-8cbd-4e82-9be5-a56bbf779fae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-608dff01-a538-4288-851e-a0b189944b18' class='xr-var-data-in' type='checkbox'><label for='data-608dff01-a538-4288-851e-a0b189944b18' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-0a12ccc9-49c5-4090-8810-e4a0133ed1d2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0a12ccc9-49c5-4090-8810-e4a0133ed1d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d5f26183-f134-46b3-8ab7-f1501eafa1b2' class='xr-var-data-in' type='checkbox'><label for='data-d5f26183-f134-46b3-8ab7-f1501eafa1b2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3321,7 +3321,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-988699a3-3fb2-44f7-a356-052d8d7fc74e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-988699a3-3fb2-44f7-a356-052d8d7fc74e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-301ee11f-1720-4d33-b7ac-8f44b3c00fbf' class='xr-var-data-in' type='checkbox'><label for='data-301ee11f-1720-4d33-b7ac-8f44b3c00fbf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-dff350b5-c11b-4397-b7b0-a03134086baa' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-dff350b5-c11b-4397-b7b0-a03134086baa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-871b5edc-11a0-49c3-9e7f-f548ccd9efaf' class='xr-var-data-in' type='checkbox'><label for='data-871b5edc-11a0-49c3-9e7f-f548ccd9efaf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3401,7 +3401,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-b8504846-5375-409e-b7db-9b53297c0692' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b8504846-5375-409e-b7db-9b53297c0692' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-079839be-0778-40d8-bff8-cc32089094b8' class='xr-var-data-in' type='checkbox'><label for='data-079839be-0778-40d8-bff8-cc32089094b8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-8a0e469d-ebdd-436e-b8a2-54f7c21679f0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8a0e469d-ebdd-436e-b8a2-54f7c21679f0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a5488d91-7297-4bb8-a819-ad1461e7fc8f' class='xr-var-data-in' type='checkbox'><label for='data-a5488d91-7297-4bb8-a819-ad1461e7fc8f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3457,7 +3457,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-2e599620-a612-42cf-b962-5568642af382' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2e599620-a612-42cf-b962-5568642af382' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3953b89c-2e9f-48c3-ac2c-3d51a5adcbe2' class='xr-var-data-in' type='checkbox'><label for='data-3953b89c-2e9f-48c3-ac2c-3d51a5adcbe2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-84e6db11-1b5f-47d8-81f8-cc2e4b3b18c5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-84e6db11-1b5f-47d8-81f8-cc2e4b3b18c5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0dccce59-c24b-4472-98ec-99eb0ae6c678' class='xr-var-data-in' type='checkbox'><label for='data-0dccce59-c24b-4472-98ec-99eb0ae6c678' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3512,7 +3512,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-0b57ae9c-c692-485c-b41d-0257afb568ef' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0b57ae9c-c692-485c-b41d-0257afb568ef' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-459f628f-0f7e-4d6d-b287-09354b4bcc15' class='xr-var-data-in' type='checkbox'><label for='data-459f628f-0f7e-4d6d-b287-09354b4bcc15' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-1bd4fa39-c19d-46cd-9592-9d60b8ecdedc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1bd4fa39-c19d-46cd-9592-9d60b8ecdedc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-72217cd8-e6cf-4ff9-a94b-a980cb879c9f' class='xr-var-data-in' type='checkbox'><label for='data-72217cd8-e6cf-4ff9-a94b-a980cb879c9f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3567,7 +3567,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-88312952-c61b-4fb7-999c-71798b365d01' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-88312952-c61b-4fb7-999c-71798b365d01' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2379d716-757c-4b51-b116-047d048606cd' class='xr-var-data-in' type='checkbox'><label for='data-2379d716-757c-4b51-b116-047d048606cd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-d5b8fc48-6856-4226-8da1-c644a7e13916' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d5b8fc48-6856-4226-8da1-c644a7e13916' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-79a8fc1a-c865-47a3-a623-22de61e9be51' class='xr-var-data-in' type='checkbox'><label for='data-79a8fc1a-c865-47a3-a623-22de61e9be51' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3622,7 +3622,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-1abec1e6-be2a-4b9c-8d55-7fb6d75b9803' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1abec1e6-be2a-4b9c-8d55-7fb6d75b9803' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-01e731e9-f5a0-495c-968f-9253be001971' class='xr-var-data-in' type='checkbox'><label for='data-01e731e9-f5a0-495c-968f-9253be001971' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-8ae605d4-0561-4212-a783-a63e32c43878' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8ae605d4-0561-4212-a783-a63e32c43878' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b8cc4a68-9d5e-4460-b5c1-781395154ec2' class='xr-var-data-in' type='checkbox'><label for='data-b8cc4a68-9d5e-4460-b5c1-781395154ec2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3678,7 +3678,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-9693309a-b98a-49c8-8084-40aeece4ccc1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9693309a-b98a-49c8-8084-40aeece4ccc1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1b4467f6-d0dc-41d6-8e27-2aa235b6e051' class='xr-var-data-in' type='checkbox'><label for='data-1b4467f6-d0dc-41d6-8e27-2aa235b6e051' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-71f9f2e1-ee00-4b3b-9e81-52c75a7d1dc0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-71f9f2e1-ee00-4b3b-9e81-52c75a7d1dc0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f441c259-f341-43fb-9dff-da9fc00e276e' class='xr-var-data-in' type='checkbox'><label for='data-f441c259-f341-43fb-9dff-da9fc00e276e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3734,7 +3734,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-93d7d6f0-cfa3-4a42-aae6-e8171fc6ea20' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-93d7d6f0-cfa3-4a42-aae6-e8171fc6ea20' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-079b4551-b68c-432a-b294-a79b10f2f169' class='xr-var-data-in' type='checkbox'><label for='data-079b4551-b68c-432a-b294-a79b10f2f169' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-67a7a114-ce60-4a82-9898-150657968cb7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-67a7a114-ce60-4a82-9898-150657968cb7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a008cf58-b575-44ee-9f5d-c7ea8a4f1da5' class='xr-var-data-in' type='checkbox'><label for='data-a008cf58-b575-44ee-9f5d-c7ea8a4f1da5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3790,7 +3790,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-268ab3ed-628e-49e1-b1ea-dd97889aae2e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-268ab3ed-628e-49e1-b1ea-dd97889aae2e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2c914284-fb39-45d3-a8b4-93507150ace6' class='xr-var-data-in' type='checkbox'><label for='data-2c914284-fb39-45d3-a8b4-93507150ace6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-5315f525-1d05-433f-bc7f-ada714a61932' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5315f525-1d05-433f-bc7f-ada714a61932' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2dc78a5b-4539-469e-b0e5-f6055fab6d34' class='xr-var-data-in' type='checkbox'><label for='data-2dc78a5b-4539-469e-b0e5-f6055fab6d34' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3846,7 +3846,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-a18bb27f-df23-43e9-ae0a-a03ac2b67b7b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a18bb27f-df23-43e9-ae0a-a03ac2b67b7b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f323bc2-5a5e-403f-9e85-0670bdf3c12a' class='xr-var-data-in' type='checkbox'><label for='data-9f323bc2-5a5e-403f-9e85-0670bdf3c12a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-c0292020-6b51-4fc2-aff3-9668abc078b5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c0292020-6b51-4fc2-aff3-9668abc078b5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f5121510-4186-4d4a-b4a8-4d0fceeba3d4' class='xr-var-data-in' type='checkbox'><label for='data-f5121510-4186-4d4a-b4a8-4d0fceeba3d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3902,7 +3902,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d3e42834-887a-4eb2-8e08-23e7de4d16ed' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d3e42834-887a-4eb2-8e08-23e7de4d16ed' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9b54895b-6465-404a-8f63-121550addd82' class='xr-var-data-in' type='checkbox'><label for='data-9b54895b-6465-404a-8f63-121550addd82' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-aa1655c5-211e-455b-9d3a-a1a0d71f3b0d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-aa1655c5-211e-455b-9d3a-a1a0d71f3b0d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-308e730e-1556-4f55-80f8-b84e180113f3' class='xr-var-data-in' type='checkbox'><label for='data-308e730e-1556-4f55-80f8-b84e180113f3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3958,7 +3958,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-afab50db-3f43-4462-887b-0511f59b523a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-afab50db-3f43-4462-887b-0511f59b523a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8c65b29b-1317-4542-942b-72db89237b47' class='xr-var-data-in' type='checkbox'><label for='data-8c65b29b-1317-4542-942b-72db89237b47' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-a2f8afe3-904d-4787-9b5f-3fb78bb9d68a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a2f8afe3-904d-4787-9b5f-3fb78bb9d68a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b7b8a104-aac9-4592-a18d-e409c06dd716' class='xr-var-data-in' type='checkbox'><label for='data-b7b8a104-aac9-4592-a18d-e409c06dd716' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -4014,7 +4014,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ef7f5ac9-e70e-4dca-8ed6-5470141f732e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ef7f5ac9-e70e-4dca-8ed6-5470141f732e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1d2dcfb1-ab5e-4efa-b764-30c7ee118552' class='xr-var-data-in' type='checkbox'><label for='data-1d2dcfb1-ab5e-4efa-b764-30c7ee118552' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-203aa7d7-b916-4fb1-a90b-920532291ff0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-203aa7d7-b916-4fb1-a90b-920532291ff0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a7a0172e-6a7f-41a1-9954-dd8f1478525c' class='xr-var-data-in' type='checkbox'><label for='data-a7a0172e-6a7f-41a1-9954-dd8f1478525c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -4070,7 +4070,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-d41556a1-3744-4d62-a61e-9d8733aadec3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d41556a1-3744-4d62-a61e-9d8733aadec3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-22a68504-dfdd-4f18-bd46-66a83c1d6300' class='xr-var-data-in' type='checkbox'><label for='data-22a68504-dfdd-4f18-bd46-66a83c1d6300' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-907ea426-9fc7-44dd-84b2-579c14d1e08c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-907ea426-9fc7-44dd-84b2-579c14d1e08c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7661fdc4-342a-4b13-a8c1-2dc76d845b10' class='xr-var-data-in' type='checkbox'><label for='data-7661fdc4-342a-4b13-a8c1-2dc76d845b10' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
        &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;,
@@ -4101,7 +4101,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-50af3ad4-8878-4bac-ae76-2e965957d3e5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-50af3ad4-8878-4bac-ae76-2e965957d3e5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7044790c-2cf1-4566-9155-a40b496fd384' class='xr-var-data-in' type='checkbox'><label for='data-7044790c-2cf1-4566-9155-a40b496fd384' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-81a8e300-8269-4556-810e-69f37e9fe88a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-81a8e300-8269-4556-810e-69f37e9fe88a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3b9eb615-8cfe-48fe-b96a-0f6a3a71b7c9' class='xr-var-data-in' type='checkbox'><label for='data-3b9eb615-8cfe-48fe-b96a-0f6a3a71b7c9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;,
@@ -4132,7 +4132,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-668edf43-97aa-4d1e-954e-3a4bdfa9f54c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-668edf43-97aa-4d1e-954e-3a4bdfa9f54c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e40fc3e8-826c-4df3-9ba0-d36ac063d2c2' class='xr-var-data-in' type='checkbox'><label for='data-e40fc3e8-826c-4df3-9ba0-d36ac063d2c2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-b25c0c96-b17e-46af-876b-0e3ee268f911' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b25c0c96-b17e-46af-876b-0e3ee268f911' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b7e1a86b-f55d-4218-bc97-f90baf925532' class='xr-var-data-in' type='checkbox'><label for='data-b7e1a86b-f55d-4218-bc97-f90baf925532' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
         True, False, False,  True,  True, False, False, False, False,
         True, False, False,  True, False,  True, False, False, False,
         True,  True,  True, False,  True,  True,  True, False,  True,
@@ -4163,7 +4163,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        False,  True, False, False,  True,  True, False, False, False,
         True, False,  True,  True,  True, False,  True,  True, False,
         True, False, False,  True,  True,  True,  True,  True, False,
-       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-6cbc8d4d-7cbe-40ca-9f66-43c2e7601c23' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6cbc8d4d-7cbe-40ca-9f66-43c2e7601c23' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e66471b8-d168-4236-ab4e-088e9ad91a5e' class='xr-var-data-in' type='checkbox'><label for='data-e66471b8-d168-4236-ab4e-088e9ad91a5e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
+       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-0961f48b-f1b3-4edf-abe1-4ffa63a59863' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0961f48b-f1b3-4edf-abe1-4ffa63a59863' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3ae3619f-7e38-4c7c-9fa9-330be2d55bcf' class='xr-var-data-in' type='checkbox'><label for='data-3ae3619f-7e38-4c7c-9fa9-330be2d55bcf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
        False,  True, False,  True,  True,  True, False, False, False,
        False,  True,  True,  True,  True,  True,  True, False,  True,
         True,  True, False,  True,  True, False,  True, False, False,
@@ -4194,7 +4194,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        False, False,  True, False, False,  True,  True, False,  True,
         True, False, False, False, False,  True,  True,  True,  True,
         True,  True,  True, False, False,  True, False, False,  True,
-        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-bd2bf172-cb08-438f-9978-9496f0a5dddf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bd2bf172-cb08-438f-9978-9496f0a5dddf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bacb1631-91db-477c-983c-a7bb1ccd375b' class='xr-var-data-in' type='checkbox'><label for='data-bacb1631-91db-477c-983c-a7bb1ccd375b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
+        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-d7ce4e8f-5ca8-4eed-934f-3f559640ee48' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d7ce4e8f-5ca8-4eed-934f-3f559640ee48' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b12a17e1-2461-41b5-b18c-840f12f788fb' class='xr-var-data-in' type='checkbox'><label for='data-b12a17e1-2461-41b5-b18c-840f12f788fb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
        7, 5, 1, 5, 5, 5, 4, 4, 5, 5, 5, 6, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5,
        5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5, 5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4,
        6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5, 4, 4, 5, 8, 3, 4, 4, 4, 7, 5, 4,
@@ -4206,7 +4206,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        4, 5, 3, 5, 6, 5, 4, 3, 8, 2, 4, 4, 6, 8, 4, 3, 4, 3, 2, 5, 6, 6,
        4, 3, 5, 7, 4, 2, 5, 5, 6, 3, 2, 4, 4, 6, 5, 6, 5, 7, 2, 4, 2, 1,
        5, 3, 5, 3, 5, 2, 4, 9, 6, 4, 3, 4, 4, 6, 6, 7, 6, 6, 3, 4, 3, 6,
-       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e8ddf2bf-d6f7-4c94-88a6-f91942d0aab2' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e8ddf2bf-d6f7-4c94-88a6-f91942d0aab2' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-0f57895a-60d3-44b8-a698-8c6ac8109ebc' class='xr-section-summary-in' type='checkbox'  ><label for='section-0f57895a-60d3-44b8-a698-8c6ac8109ebc' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-cf54574e-bdc8-41de-bcfc-72c635862558' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-cf54574e-bdc8-41de-bcfc-72c635862558' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-00d6f885-39ed-4d39-b536-250205c0b583' class='xr-section-summary-in' type='checkbox'  ><label for='section-00d6f885-39ed-4d39-b536-250205c0b583' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -4866,7 +4866,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
     isFemale              (samples) bool 284B False True False ... False True
     PurpleHair            (samples) bool 284B False False False ... True True
     CaffeineConsumption   (samples) int64 2kB 4 4 4 3 6 2 4 2 ... 6 4 6 4 6 5 5
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-1058bfea-79c0-4093-98d1-c77cb6cc3807' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-1058bfea-79c0-4093-98d1-c77cb6cc3807' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-2ea9e483-e62c-4a79-aa8b-b6e3abf19f04' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2ea9e483-e62c-4a79-aa8b-b6e3abf19f04' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-0ee806e0-fca7-4eba-b5eb-f3e6ae45449c' class='xr-section-summary-in' type='checkbox'  checked><label for='section-0ee806e0-fca7-4eba-b5eb-f3e6ae45449c' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-2dfcb0a9-f0ba-4065-b5d6-c95983206c95' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2dfcb0a9-f0ba-4065-b5d6-c95983206c95' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8f5c3100-85fe-4dbe-87f9-bdb7564c8a47' class='xr-var-data-in' type='checkbox'><label for='data-8f5c3100-85fe-4dbe-87f9-bdb7564c8a47' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-2353da1f-ada1-43c1-9580-b9cfe1aede50' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2353da1f-ada1-43c1-9580-b9cfe1aede50' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-c79beb76-2020-41b8-be93-edc07b0533a5' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c79beb76-2020-41b8-be93-edc07b0533a5' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-4017ab0c-71b1-4ecd-81cb-787a87f6fc29' class='xr-section-summary-in' type='checkbox'  checked><label for='section-4017ab0c-71b1-4ecd-81cb-787a87f6fc29' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-4d9c98b7-c06a-499b-abbe-b072ac70ffbf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4d9c98b7-c06a-499b-abbe-b072ac70ffbf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6d70c715-5493-421e-a2b7-83718cf653f2' class='xr-var-data-in' type='checkbox'><label for='data-6d70c715-5493-421e-a2b7-83718cf653f2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -4946,7 +4946,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-c4a2177d-5435-4c71-b8dc-abcd2100b3df' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c4a2177d-5435-4c71-b8dc-abcd2100b3df' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e4bfe84c-69c3-45fa-ab7f-077201b387ec' class='xr-var-data-in' type='checkbox'><label for='data-e4bfe84c-69c3-45fa-ab7f-077201b387ec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-859fd635-49c6-40d3-9502-d97665be220b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-859fd635-49c6-40d3-9502-d97665be220b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-898c0ef3-eab8-4588-82e3-5183e5de6ab7' class='xr-var-data-in' type='checkbox'><label for='data-898c0ef3-eab8-4588-82e3-5183e5de6ab7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5002,7 +5002,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-8046fbd9-2cdf-4996-b468-8fdd504fa65a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8046fbd9-2cdf-4996-b468-8fdd504fa65a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a4c3093e-07a6-4327-9923-ee3dd3524ba7' class='xr-var-data-in' type='checkbox'><label for='data-a4c3093e-07a6-4327-9923-ee3dd3524ba7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-0676ff7a-29cc-4ac3-b20d-5d6aadef25af' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0676ff7a-29cc-4ac3-b20d-5d6aadef25af' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-15d69221-0471-40f8-8a3c-23dc4351e48e' class='xr-var-data-in' type='checkbox'><label for='data-15d69221-0471-40f8-8a3c-23dc4351e48e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5058,7 +5058,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-83d5b9d5-5aa8-40bd-a285-c2a89f4453e7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-83d5b9d5-5aa8-40bd-a285-c2a89f4453e7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cad34aa2-71fb-4023-82bc-e6c8908977ff' class='xr-var-data-in' type='checkbox'><label for='data-cad34aa2-71fb-4023-82bc-e6c8908977ff' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-9f2c3c43-e728-4d15-b7c0-5620cfaf609d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9f2c3c43-e728-4d15-b7c0-5620cfaf609d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2eb30e9d-4b2c-42fe-a2b9-5b9fea711742' class='xr-var-data-in' type='checkbox'><label for='data-2eb30e9d-4b2c-42fe-a2b9-5b9fea711742' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5138,7 +5138,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-bdee678b-42e8-4dfd-8a37-b9d40f4e7821' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-bdee678b-42e8-4dfd-8a37-b9d40f4e7821' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-76d2910a-d1a7-4cee-9915-51397921f8d2' class='xr-var-data-in' type='checkbox'><label for='data-76d2910a-d1a7-4cee-9915-51397921f8d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-638fe9cc-9457-4095-bade-d09479d31be6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-638fe9cc-9457-4095-bade-d09479d31be6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-23d73c70-d389-42d8-b75f-1b1b78b1010c' class='xr-var-data-in' type='checkbox'><label for='data-23d73c70-d389-42d8-b75f-1b1b78b1010c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5218,7 +5218,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-25d137aa-d8d4-4541-9cea-f1726cf95b53' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-25d137aa-d8d4-4541-9cea-f1726cf95b53' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-62ad62cd-d884-47c6-b677-69dbb868bedc' class='xr-var-data-in' type='checkbox'><label for='data-62ad62cd-d884-47c6-b677-69dbb868bedc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-ed168e17-7570-4c6a-b424-226def31bd01' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ed168e17-7570-4c6a-b424-226def31bd01' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d556f768-6cfd-4598-9958-bc9cc6318f78' class='xr-var-data-in' type='checkbox'><label for='data-d556f768-6cfd-4598-9958-bc9cc6318f78' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5274,7 +5274,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-68e81574-251a-4031-b4da-5d4e5865634a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-68e81574-251a-4031-b4da-5d4e5865634a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b197fd93-ff58-47f6-a6d5-fa8624e13c63' class='xr-var-data-in' type='checkbox'><label for='data-b197fd93-ff58-47f6-a6d5-fa8624e13c63' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-45605696-68fb-4af6-98b8-c144e9317926' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-45605696-68fb-4af6-98b8-c144e9317926' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c3ea973c-fcc1-4be9-99b6-2447ecc36517' class='xr-var-data-in' type='checkbox'><label for='data-c3ea973c-fcc1-4be9-99b6-2447ecc36517' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5329,7 +5329,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-7ef3abf9-40cd-4878-81f0-f9c1cfb6dc67' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7ef3abf9-40cd-4878-81f0-f9c1cfb6dc67' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a4739317-75cf-41d5-9395-ab17f65e4a6b' class='xr-var-data-in' type='checkbox'><label for='data-a4739317-75cf-41d5-9395-ab17f65e4a6b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-7a2b8649-0da6-40ad-b0b7-92eb6b0671b3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7a2b8649-0da6-40ad-b0b7-92eb6b0671b3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e44f1709-da45-4457-a369-80cae87277ca' class='xr-var-data-in' type='checkbox'><label for='data-e44f1709-da45-4457-a369-80cae87277ca' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5384,7 +5384,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-fa711335-8666-4adc-89f8-65005660cec7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fa711335-8666-4adc-89f8-65005660cec7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ce3fdf98-993f-4e2c-a8dc-2a9c0980bfaa' class='xr-var-data-in' type='checkbox'><label for='data-ce3fdf98-993f-4e2c-a8dc-2a9c0980bfaa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-96c45fe1-4038-4822-b923-8a09f808a651' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-96c45fe1-4038-4822-b923-8a09f808a651' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fa8f3d42-34f1-4670-bf1c-da4aea4c7aa5' class='xr-var-data-in' type='checkbox'><label for='data-fa8f3d42-34f1-4670-bf1c-da4aea4c7aa5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5439,7 +5439,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-b2e4ff85-7407-4dc0-a1eb-b014ea9b0f5f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b2e4ff85-7407-4dc0-a1eb-b014ea9b0f5f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8a7f0f3c-7626-477f-9e24-64251bba7955' class='xr-var-data-in' type='checkbox'><label for='data-8a7f0f3c-7626-477f-9e24-64251bba7955' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-269840c0-16d9-47a5-91f8-97d1255f0fe0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-269840c0-16d9-47a5-91f8-97d1255f0fe0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0e04475e-b510-431a-b6d2-d7f5e6bde883' class='xr-var-data-in' type='checkbox'><label for='data-0e04475e-b510-431a-b6d2-d7f5e6bde883' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5495,7 +5495,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-2c3e10c1-a49b-46ac-b902-6d1a7d74f9aa' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2c3e10c1-a49b-46ac-b902-6d1a7d74f9aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9be4cdc8-fa2d-40ac-be35-9b0236d31799' class='xr-var-data-in' type='checkbox'><label for='data-9be4cdc8-fa2d-40ac-be35-9b0236d31799' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-dad838d8-5925-4b81-a310-df5f8ed395cb' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-dad838d8-5925-4b81-a310-df5f8ed395cb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c255dbd6-c740-49cb-9486-74250fdfb644' class='xr-var-data-in' type='checkbox'><label for='data-c255dbd6-c740-49cb-9486-74250fdfb644' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5551,7 +5551,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-5dee4f57-58f2-49b4-98e0-ac1d1e53434a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5dee4f57-58f2-49b4-98e0-ac1d1e53434a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d6106c8c-87bd-4aa2-8456-1f3d40f59c6c' class='xr-var-data-in' type='checkbox'><label for='data-d6106c8c-87bd-4aa2-8456-1f3d40f59c6c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-7724fc6c-069d-480f-a3f1-2bfe91263603' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7724fc6c-069d-480f-a3f1-2bfe91263603' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-873e1aa5-c749-46f0-8be8-63c9a4db29c2' class='xr-var-data-in' type='checkbox'><label for='data-873e1aa5-c749-46f0-8be8-63c9a4db29c2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5607,7 +5607,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-20f79610-3f2f-46d4-a582-078275dc1ce4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-20f79610-3f2f-46d4-a582-078275dc1ce4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1278d2e1-7c55-4c7a-af2f-076c4ab9c115' class='xr-var-data-in' type='checkbox'><label for='data-1278d2e1-7c55-4c7a-af2f-076c4ab9c115' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-c290884a-327f-441e-9dc5-68fc2cedaa1f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c290884a-327f-441e-9dc5-68fc2cedaa1f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-850aecf8-a110-4a7d-8eb8-5f9a4a02561f' class='xr-var-data-in' type='checkbox'><label for='data-850aecf8-a110-4a7d-8eb8-5f9a4a02561f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5663,7 +5663,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ef4786ea-5ecf-4c1d-b8e3-07ac32d3658e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ef4786ea-5ecf-4c1d-b8e3-07ac32d3658e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-43272b4b-0ef1-4506-9c41-92ad8e3cd8f1' class='xr-var-data-in' type='checkbox'><label for='data-43272b4b-0ef1-4506-9c41-92ad8e3cd8f1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-314c82ba-b5d5-4495-b43e-b23b8f192574' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-314c82ba-b5d5-4495-b43e-b23b8f192574' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d1aefb48-12d7-4671-8aec-7182a994f449' class='xr-var-data-in' type='checkbox'><label for='data-d1aefb48-12d7-4671-8aec-7182a994f449' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5719,7 +5719,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-a6ff7218-abd3-4a4f-bd95-62b1bdd5194f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a6ff7218-abd3-4a4f-bd95-62b1bdd5194f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fe026f7f-79ac-4162-a70e-32101c13031e' class='xr-var-data-in' type='checkbox'><label for='data-fe026f7f-79ac-4162-a70e-32101c13031e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-318a8e67-ef96-4ed4-9ab7-267de7f967ed' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-318a8e67-ef96-4ed4-9ab7-267de7f967ed' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ecd60a78-02b4-4eb8-ba24-ab79d9988623' class='xr-var-data-in' type='checkbox'><label for='data-ecd60a78-02b4-4eb8-ba24-ab79d9988623' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5775,7 +5775,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-0bf371e2-fd70-4e28-8575-17fa1aaaeb08' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0bf371e2-fd70-4e28-8575-17fa1aaaeb08' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7ac6f060-9578-4ac6-bcb3-50466a391e4e' class='xr-var-data-in' type='checkbox'><label for='data-7ac6f060-9578-4ac6-bcb3-50466a391e4e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-25787df4-d5f8-4fd9-af59-a9b03a903d93' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-25787df4-d5f8-4fd9-af59-a9b03a903d93' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-613adb9c-ce67-4b18-9ce6-f3daad0d5983' class='xr-var-data-in' type='checkbox'><label for='data-613adb9c-ce67-4b18-9ce6-f3daad0d5983' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5831,7 +5831,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-e38bf0a7-d7d5-45d3-b74d-52c00c63a381' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e38bf0a7-d7d5-45d3-b74d-52c00c63a381' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4eabaa16-ac7d-439f-8175-ad93f9e07eb0' class='xr-var-data-in' type='checkbox'><label for='data-4eabaa16-ac7d-439f-8175-ad93f9e07eb0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-33cc00fe-8a42-4ba4-b57a-e1efa6fad702' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-33cc00fe-8a42-4ba4-b57a-e1efa6fad702' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-49cd7700-70b2-49ce-afc4-eb6f6201ec7b' class='xr-var-data-in' type='checkbox'><label for='data-49cd7700-70b2-49ce-afc4-eb6f6201ec7b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5887,7 +5887,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-279bb718-8b93-4d26-80fc-3435f5cedfe0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-279bb718-8b93-4d26-80fc-3435f5cedfe0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6e866c10-57db-402d-a52e-ff46b0cb5a99' class='xr-var-data-in' type='checkbox'><label for='data-6e866c10-57db-402d-a52e-ff46b0cb5a99' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-d1f3bf10-7e9b-44f6-b774-fad0cfb778da' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d1f3bf10-7e9b-44f6-b774-fad0cfb778da' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d6bd69fe-565c-4467-8646-df64ac5de07f' class='xr-var-data-in' type='checkbox'><label for='data-d6bd69fe-565c-4467-8646-df64ac5de07f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
        &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;,
@@ -5918,7 +5918,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-229010f9-af56-4478-a8a9-015b2d498201' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-229010f9-af56-4478-a8a9-015b2d498201' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b4600081-53f7-413b-9b3b-83b212d7579b' class='xr-var-data-in' type='checkbox'><label for='data-b4600081-53f7-413b-9b3b-83b212d7579b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-34c545a1-7333-4f3a-91af-3848f2a5f0d1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-34c545a1-7333-4f3a-91af-3848f2a5f0d1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7299a071-e5f7-4c51-95f0-287d010c66ee' class='xr-var-data-in' type='checkbox'><label for='data-7299a071-e5f7-4c51-95f0-287d010c66ee' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;,
@@ -5949,7 +5949,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-74267360-9a7d-4cbd-ac70-1145186bd9ae' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-74267360-9a7d-4cbd-ac70-1145186bd9ae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-03f833ae-55a6-4309-9b1b-56dc7899cc99' class='xr-var-data-in' type='checkbox'><label for='data-03f833ae-55a6-4309-9b1b-56dc7899cc99' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-d8cfd2e4-b8b0-4812-8250-917790ac760a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d8cfd2e4-b8b0-4812-8250-917790ac760a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-24459c21-98b4-4918-be6c-deda4198fd30' class='xr-var-data-in' type='checkbox'><label for='data-24459c21-98b4-4918-be6c-deda4198fd30' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
         True, False, False,  True,  True, False, False, False, False,
         True, False, False,  True, False,  True, False, False, False,
         True,  True,  True, False,  True,  True,  True, False,  True,
@@ -5980,7 +5980,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False,  True, False, False,  True,  True, False, False, False,
         True, False,  True,  True,  True, False,  True,  True, False,
         True, False, False,  True,  True,  True,  True,  True, False,
-       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-b4c83c4d-89e3-4028-a7cd-c617a0e76231' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b4c83c4d-89e3-4028-a7cd-c617a0e76231' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eb6c4190-6ae3-4527-8c26-8f1b16f6f8ae' class='xr-var-data-in' type='checkbox'><label for='data-eb6c4190-6ae3-4527-8c26-8f1b16f6f8ae' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
+       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-84cbd1eb-2e58-44a7-baa7-bee787aadf39' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-84cbd1eb-2e58-44a7-baa7-bee787aadf39' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c84cc449-2412-4b2e-960d-df8c6bbd33f9' class='xr-var-data-in' type='checkbox'><label for='data-c84cc449-2412-4b2e-960d-df8c6bbd33f9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
        False,  True, False,  True,  True,  True, False, False, False,
        False,  True,  True,  True,  True,  True,  True, False,  True,
         True,  True, False,  True,  True, False,  True, False, False,
@@ -6011,7 +6011,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False, False,  True, False, False,  True,  True, False,  True,
         True, False, False, False, False,  True,  True,  True,  True,
         True,  True,  True, False, False,  True, False, False,  True,
-        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-cbf242e8-fe95-4602-953c-2e006adb10e1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cbf242e8-fe95-4602-953c-2e006adb10e1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6b65dad9-f083-4214-9ae0-802b21e7690f' class='xr-var-data-in' type='checkbox'><label for='data-6b65dad9-f083-4214-9ae0-802b21e7690f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
+        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-ab67cd40-79b3-4aed-b592-2fbcd13634b8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ab67cd40-79b3-4aed-b592-2fbcd13634b8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1fb645f7-5670-447b-9f8f-1b737caa73e1' class='xr-var-data-in' type='checkbox'><label for='data-1fb645f7-5670-447b-9f8f-1b737caa73e1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
        7, 5, 1, 5, 5, 5, 4, 4, 5, 5, 5, 6, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5,
        5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5, 5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4,
        6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5, 4, 4, 5, 8, 3, 4, 4, 4, 7, 5, 4,
@@ -6023,7 +6023,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        4, 5, 3, 5, 6, 5, 4, 3, 8, 2, 4, 4, 6, 8, 4, 3, 4, 3, 2, 5, 6, 6,
        4, 3, 5, 7, 4, 2, 5, 5, 6, 3, 2, 4, 4, 6, 5, 6, 5, 7, 2, 4, 2, 1,
        5, 3, 5, 3, 5, 2, 4, 9, 6, 4, 3, 4, 4, 6, 6, 7, 6, 6, 3, 4, 3, 6,
-       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-456ef5ea-5540-4c2b-9a16-f3cda93492d1' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-456ef5ea-5540-4c2b-9a16-f3cda93492d1' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-f067ace2-43de-465b-9ad0-f558b6067306' class='xr-section-summary-in' type='checkbox'  ><label for='section-f067ace2-43de-465b-9ad0-f558b6067306' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-6bf9807d-4c7f-4951-9e25-0bc4575214b8' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-6bf9807d-4c7f-4951-9e25-0bc4575214b8' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-dff1c6dc-62a0-4c7b-86cc-899405d52a1d' class='xr-section-summary-in' type='checkbox'  ><label for='section-dff1c6dc-62a0-4c7b-86cc-899405d52a1d' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -6533,7 +6533,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
     isFemale              (samples) bool 284B False True False ... False True
     PurpleHair            (samples) bool 284B False False False ... True True
     CaffeineConsumption   (samples) int64 2kB 4 4 4 3 6 2 4 2 ... 6 4 6 4 6 5 5
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-8b0289c9-5ec2-44a6-9f73-1a5f20ebaa7a' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-8b0289c9-5ec2-44a6-9f73-1a5f20ebaa7a' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-390b4e5e-e766-4b86-9d4d-00dd98144615' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-390b4e5e-e766-4b86-9d4d-00dd98144615' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-0e1211ae-e93c-4155-93dc-1d69dfe22b8c' class='xr-section-summary-in' type='checkbox'  checked><label for='section-0e1211ae-e93c-4155-93dc-1d69dfe22b8c' class='xr-section-summary' >Data variables: <span>(28)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-971fcc21-6c78-4b79-8d5c-f4cd6aaa1c0e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-971fcc21-6c78-4b79-8d5c-f4cd6aaa1c0e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-90fe4171-1dc7-4345-ad37-4937bd3fb160' class='xr-var-data-in' type='checkbox'><label for='data-90fe4171-1dc7-4345-ad37-4937bd3fb160' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-62776dba-1355-4527-a54a-1320ee584649' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-62776dba-1355-4527-a54a-1320ee584649' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-e25b8e3e-38c5-4f51-a6ca-c086b165455e' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e25b8e3e-38c5-4f51-a6ca-c086b165455e' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-8724d25d-b794-4cb4-b1e0-8691ddf9c75f' class='xr-section-summary-in' type='checkbox'  checked><label for='section-8724d25d-b794-4cb4-b1e0-8691ddf9c75f' class='xr-section-summary' >Data variables: <span>(28)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-b27ab197-f646-4302-8534-1541c4909e84' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b27ab197-f646-4302-8534-1541c4909e84' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1cd6b31a-ec40-4ac6-8af5-a0fad4dead06' class='xr-var-data-in' type='checkbox'><label for='data-1cd6b31a-ec40-4ac6-8af5-a0fad4dead06' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6559,7 +6559,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -6588,7 +6588,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-5ba57270-1619-41fa-b670-fefc7fe45c43' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5ba57270-1619-41fa-b670-fefc7fe45c43' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9b304b6a-8982-44fa-baa2-b73bf6977789' class='xr-var-data-in' type='checkbox'><label for='data-9b304b6a-8982-44fa-baa2-b73bf6977789' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-734b5aca-34e7-4d2f-bf81-adcb630bb796' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-734b5aca-34e7-4d2f-bf81-adcb630bb796' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f370a9a7-b9b0-4711-a091-0001b09307c2' class='xr-var-data-in' type='checkbox'><label for='data-f370a9a7-b9b0-4711-a091-0001b09307c2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6614,7 +6614,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 7 graph layers </td>
+                        <td colspan="2"> 1 chunks in 10 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -6643,7 +6643,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-0e148b6f-c39c-432c-b21b-6b5499dce53a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0e148b6f-c39c-432c-b21b-6b5499dce53a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8972f0aa-9b0c-49cb-b56a-84c6432a13f1' class='xr-var-data-in' type='checkbox'><label for='data-8972f0aa-9b0c-49cb-b56a-84c6432a13f1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-36969d51-653a-4221-b72c-3a1114362432' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-36969d51-653a-4221-b72c-3a1114362432' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c7005258-dc43-4df8-afff-086e4e90eaff' class='xr-var-data-in' type='checkbox'><label for='data-c7005258-dc43-4df8-afff-086e4e90eaff' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6669,7 +6669,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 5 graph layers </td>
+                        <td colspan="2"> 1 chunks in 7 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -6698,7 +6698,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-ff0058e9-96b2-479a-9485-5ee13da0fa5c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ff0058e9-96b2-479a-9485-5ee13da0fa5c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-121bf84f-6341-44df-befc-397f64e2cff3' class='xr-var-data-in' type='checkbox'><label for='data-121bf84f-6341-44df-befc-397f64e2cff3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-33c76c52-583a-46ec-9d93-391674bd1421' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-33c76c52-583a-46ec-9d93-391674bd1421' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f74e11a2-ce04-4431-9df5-adb6b5e9a2b8' class='xr-var-data-in' type='checkbox'><label for='data-f74e11a2-ce04-4431-9df5-adb6b5e9a2b8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6724,7 +6724,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 5 graph layers </td>
+                        <td colspan="2"> 1 chunks in 7 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -6753,7 +6753,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-394e0f34-a2f3-4807-8385-dea6e73268d4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-394e0f34-a2f3-4807-8385-dea6e73268d4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f6ba56b9-30a9-4294-9cb9-b5151fdb0ba3' class='xr-var-data-in' type='checkbox'><label for='data-f6ba56b9-30a9-4294-9cb9-b5151fdb0ba3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-99360899-e938-425e-b57f-9bf6566ddf9b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-99360899-e938-425e-b57f-9bf6566ddf9b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c41da8cd-13a4-4af7-8720-062e92969e7c' class='xr-var-data-in' type='checkbox'><label for='data-c41da8cd-13a4-4af7-8720-062e92969e7c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6779,7 +6779,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 5 graph layers </td>
+                        <td colspan="2"> 1 chunks in 7 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -6808,7 +6808,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-af06063a-8a7b-4bed-bde9-952d45481575' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-af06063a-8a7b-4bed-bde9-952d45481575' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-545ce0e7-5a69-48d8-bb8f-bc2ac6d247cc' class='xr-var-data-in' type='checkbox'><label for='data-545ce0e7-5a69-48d8-bb8f-bc2ac6d247cc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-f8af40ce-c6c3-4e88-92d3-21c12788b019' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f8af40ce-c6c3-4e88-92d3-21c12788b019' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-808a311e-70a6-4ad6-a25e-0e1190c834c5' class='xr-var-data-in' type='checkbox'><label for='data-808a311e-70a6-4ad6-a25e-0e1190c834c5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6834,7 +6834,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 8 graph layers </td>
+                        <td colspan="2"> 1 chunks in 10 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -6863,7 +6863,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-49246e79-8a2a-427d-b174-abab8fbf7b0c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-49246e79-8a2a-427d-b174-abab8fbf7b0c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bd65db0d-83bc-4908-a755-71a6e9c6f918' class='xr-var-data-in' type='checkbox'><label for='data-bd65db0d-83bc-4908-a755-71a6e9c6f918' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-534a1ccd-aff7-4608-bed7-946f7f212356' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-534a1ccd-aff7-4608-bed7-946f7f212356' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-672658b4-f73a-4aed-9119-d4775c1743dd' class='xr-var-data-in' type='checkbox'><label for='data-672658b4-f73a-4aed-9119-d4775c1743dd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6943,7 +6943,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-baca6ec8-bf7b-4368-8995-657f4d8fd286' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-baca6ec8-bf7b-4368-8995-657f4d8fd286' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-adf77045-1a17-485b-88f5-44a2e8ad6d41' class='xr-var-data-in' type='checkbox'><label for='data-adf77045-1a17-485b-88f5-44a2e8ad6d41' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-be9d3eff-08ae-4224-852a-d9dd7a7405fa' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-be9d3eff-08ae-4224-852a-d9dd7a7405fa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-82fc3b0f-a221-4c97-8f5b-4e0f253580d4' class='xr-var-data-in' type='checkbox'><label for='data-82fc3b0f-a221-4c97-8f5b-4e0f253580d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6999,7 +6999,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-bd6dc661-44de-450a-a029-6777653d3090' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-bd6dc661-44de-450a-a029-6777653d3090' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2a07d92e-d598-430f-af9a-5740ea2df75f' class='xr-var-data-in' type='checkbox'><label for='data-2a07d92e-d598-430f-af9a-5740ea2df75f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-f6f732a5-7abf-46d5-9809-ad3634d8299b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f6f732a5-7abf-46d5-9809-ad3634d8299b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-35e7f098-6cbf-4b59-9cb4-43a063fd7ed3' class='xr-var-data-in' type='checkbox'><label for='data-35e7f098-6cbf-4b59-9cb4-43a063fd7ed3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7055,7 +7055,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-0a8333bb-75b1-4443-94e9-5dbf6da91ead' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0a8333bb-75b1-4443-94e9-5dbf6da91ead' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-37031757-4c26-44fb-9f69-df16199ad34a' class='xr-var-data-in' type='checkbox'><label for='data-37031757-4c26-44fb-9f69-df16199ad34a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-a5dbd324-5278-4d2e-9507-e34fef634a5d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a5dbd324-5278-4d2e-9507-e34fef634a5d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-91e2a53c-35a7-4598-abc9-ce79e5172d98' class='xr-var-data-in' type='checkbox'><label for='data-91e2a53c-35a7-4598-abc9-ce79e5172d98' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7135,7 +7135,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-77d45e5b-b218-41f3-b2f6-2966cb47aeaf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-77d45e5b-b218-41f3-b2f6-2966cb47aeaf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-92d043b2-71c2-4928-be02-1002465cf74d' class='xr-var-data-in' type='checkbox'><label for='data-92d043b2-71c2-4928-be02-1002465cf74d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-7ae33351-5680-4f21-9653-a1b0b5730fc8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7ae33351-5680-4f21-9653-a1b0b5730fc8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d2be447-9cff-443b-9341-009e39a8b883' class='xr-var-data-in' type='checkbox'><label for='data-9d2be447-9cff-443b-9341-009e39a8b883' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7215,7 +7215,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-ac81e30d-b985-4383-a765-f651505af8a9' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ac81e30d-b985-4383-a765-f651505af8a9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7c719c35-b91b-494d-889e-702602c8ce1d' class='xr-var-data-in' type='checkbox'><label for='data-7c719c35-b91b-494d-889e-702602c8ce1d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-1a871971-f51f-40c7-9dcb-02565e04173b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1a871971-f51f-40c7-9dcb-02565e04173b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b4cdbb75-7b33-4c58-8826-e820904889ac' class='xr-var-data-in' type='checkbox'><label for='data-b4cdbb75-7b33-4c58-8826-e820904889ac' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7271,7 +7271,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-a88c423c-5920-4564-8a2a-6feadf4ec547' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a88c423c-5920-4564-8a2a-6feadf4ec547' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d9a216e3-8f0e-49eb-94ea-54ffb4feab92' class='xr-var-data-in' type='checkbox'><label for='data-d9a216e3-8f0e-49eb-94ea-54ffb4feab92' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-38a1dc82-06c2-4547-ba78-476fdc328315' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-38a1dc82-06c2-4547-ba78-476fdc328315' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7b78d829-7a41-463e-8196-1a85683901d6' class='xr-var-data-in' type='checkbox'><label for='data-7b78d829-7a41-463e-8196-1a85683901d6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7326,7 +7326,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-d07ac74b-1a40-4b82-9990-b590d98009a2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d07ac74b-1a40-4b82-9990-b590d98009a2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3976f26f-8f91-4021-a9cf-ce19acb6df94' class='xr-var-data-in' type='checkbox'><label for='data-3976f26f-8f91-4021-a9cf-ce19acb6df94' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-65b00583-7cf6-4bb5-afb9-ef8f2fe0e8cd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-65b00583-7cf6-4bb5-afb9-ef8f2fe0e8cd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-edb115b1-a1bf-41f1-a7d1-01d219c33586' class='xr-var-data-in' type='checkbox'><label for='data-edb115b1-a1bf-41f1-a7d1-01d219c33586' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7381,7 +7381,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-002b9f57-3ba1-4d83-93f0-b5014ae60d96' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-002b9f57-3ba1-4d83-93f0-b5014ae60d96' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cdb2f101-38d9-49ab-9d1b-90ab121b5fb1' class='xr-var-data-in' type='checkbox'><label for='data-cdb2f101-38d9-49ab-9d1b-90ab121b5fb1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-b4f08cef-516d-414a-8083-d541da3fba55' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b4f08cef-516d-414a-8083-d541da3fba55' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-753fbc77-cfb2-455f-a732-c09d4adc06d7' class='xr-var-data-in' type='checkbox'><label for='data-753fbc77-cfb2-455f-a732-c09d4adc06d7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7436,7 +7436,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-95c0160b-f0e1-4ffe-b326-629a95bda6ff' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-95c0160b-f0e1-4ffe-b326-629a95bda6ff' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d0fe5816-592f-4d2b-b73d-473d75fc28f0' class='xr-var-data-in' type='checkbox'><label for='data-d0fe5816-592f-4d2b-b73d-473d75fc28f0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-4950c0c7-204a-44f8-b21b-4449ab23887d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4950c0c7-204a-44f8-b21b-4449ab23887d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f2e0d64c-b2a8-4284-8d18-33b1e90d8073' class='xr-var-data-in' type='checkbox'><label for='data-f2e0d64c-b2a8-4284-8d18-33b1e90d8073' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7492,7 +7492,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-26cb84a2-f787-4ff9-b651-0a8f387b9124' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-26cb84a2-f787-4ff9-b651-0a8f387b9124' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e58da053-4c0b-431b-871f-7bbd2a5fed36' class='xr-var-data-in' type='checkbox'><label for='data-e58da053-4c0b-431b-871f-7bbd2a5fed36' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-1781ac33-1b6e-43be-86a7-e486dd170734' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1781ac33-1b6e-43be-86a7-e486dd170734' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dd0c6c4b-61e1-4ef2-a778-10867e2be284' class='xr-var-data-in' type='checkbox'><label for='data-dd0c6c4b-61e1-4ef2-a778-10867e2be284' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7548,7 +7548,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-103322b5-e622-4348-accf-b0c0a87000c6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-103322b5-e622-4348-accf-b0c0a87000c6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3815d1cd-99cf-4821-92ec-f6aafec2c7ba' class='xr-var-data-in' type='checkbox'><label for='data-3815d1cd-99cf-4821-92ec-f6aafec2c7ba' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-1871d65f-7cad-498b-b335-942d6f0a38da' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1871d65f-7cad-498b-b335-942d6f0a38da' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cf6e3887-8c8a-4f0b-9b1f-250574f799d4' class='xr-var-data-in' type='checkbox'><label for='data-cf6e3887-8c8a-4f0b-9b1f-250574f799d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7604,7 +7604,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-419487cf-00e4-4870-9f22-b25cbc3993b7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-419487cf-00e4-4870-9f22-b25cbc3993b7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4a168a64-40f2-4ed2-be1c-f1a6d815f53e' class='xr-var-data-in' type='checkbox'><label for='data-4a168a64-40f2-4ed2-be1c-f1a6d815f53e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-43acddca-029f-4f3b-90d9-583294aac3d3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-43acddca-029f-4f3b-90d9-583294aac3d3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9e100118-7c31-4d09-aecf-6ccf7c6c0235' class='xr-var-data-in' type='checkbox'><label for='data-9e100118-7c31-4d09-aecf-6ccf7c6c0235' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7660,7 +7660,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-abb61d70-6351-485b-af73-bbb606f4cf8d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-abb61d70-6351-485b-af73-bbb606f4cf8d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dae7090d-ce5b-4a4a-9434-f2e990023f4c' class='xr-var-data-in' type='checkbox'><label for='data-dae7090d-ce5b-4a4a-9434-f2e990023f4c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-071fd376-3d7d-41cf-a2dc-3b9edee0d11c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-071fd376-3d7d-41cf-a2dc-3b9edee0d11c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7b70e639-acfc-48ba-ae78-567919162bb8' class='xr-var-data-in' type='checkbox'><label for='data-7b70e639-acfc-48ba-ae78-567919162bb8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7716,7 +7716,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-56abe352-4b5e-4c79-84f7-900acce0ff4c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-56abe352-4b5e-4c79-84f7-900acce0ff4c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0e2d5882-99c0-4872-a4d7-2e29edb36ebe' class='xr-var-data-in' type='checkbox'><label for='data-0e2d5882-99c0-4872-a4d7-2e29edb36ebe' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-cefc9c7d-9a3c-43c8-b83a-8c6e70a84be1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cefc9c7d-9a3c-43c8-b83a-8c6e70a84be1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-39af341c-3b6d-42a5-9034-51ff87838b4d' class='xr-var-data-in' type='checkbox'><label for='data-39af341c-3b6d-42a5-9034-51ff87838b4d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7772,7 +7772,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-87c4c124-a67a-4595-a4af-84abeb1d8f77' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-87c4c124-a67a-4595-a4af-84abeb1d8f77' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f4a2604b-a4af-469d-a892-9b3a5df79a34' class='xr-var-data-in' type='checkbox'><label for='data-f4a2604b-a4af-469d-a892-9b3a5df79a34' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-af009bcf-a1d1-461e-87f6-1b36b8208a39' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-af009bcf-a1d1-461e-87f6-1b36b8208a39' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bba404aa-6ec2-4555-95d1-8d4baeb89bdf' class='xr-var-data-in' type='checkbox'><label for='data-bba404aa-6ec2-4555-95d1-8d4baeb89bdf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7828,7 +7828,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-995094a3-f322-4c3c-b9b0-0ce632df9c20' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-995094a3-f322-4c3c-b9b0-0ce632df9c20' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf0cef3e-7e02-43d4-bef7-6a4a7dd870cd' class='xr-var-data-in' type='checkbox'><label for='data-bf0cef3e-7e02-43d4-bef7-6a4a7dd870cd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-8e97fdd9-4bae-46bc-a19b-c99ec10c09dc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8e97fdd9-4bae-46bc-a19b-c99ec10c09dc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f0d82c90-e6a3-47af-a8e1-5ad74deaad54' class='xr-var-data-in' type='checkbox'><label for='data-f0d82c90-e6a3-47af-a8e1-5ad74deaad54' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7884,7 +7884,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-e029a264-e48d-4e43-82f4-c327b35a0389' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e029a264-e48d-4e43-82f4-c327b35a0389' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0d7e84a2-831b-4f5a-9cdd-f6dd3ab22783' class='xr-var-data-in' type='checkbox'><label for='data-0d7e84a2-831b-4f5a-9cdd-f6dd3ab22783' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-3fb127b2-ff16-4dcd-a828-a0de82c8562a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3fb127b2-ff16-4dcd-a828-a0de82c8562a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-00e480ad-8f4e-4f98-9be4-7785dee995b4' class='xr-var-data-in' type='checkbox'><label for='data-00e480ad-8f4e-4f98-9be4-7785dee995b4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
        &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;,
@@ -7915,7 +7915,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-ccaa1c95-80dc-4909-829e-9218ceb87ee3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ccaa1c95-80dc-4909-829e-9218ceb87ee3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-51c79dc2-5a47-4fe8-a303-73d68c8989db' class='xr-var-data-in' type='checkbox'><label for='data-51c79dc2-5a47-4fe8-a303-73d68c8989db' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-a59578e6-1ee2-44c7-8c5d-5851daead3c3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a59578e6-1ee2-44c7-8c5d-5851daead3c3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1bc338a3-b9b8-4983-b17c-9dc364e63396' class='xr-var-data-in' type='checkbox'><label for='data-1bc338a3-b9b8-4983-b17c-9dc364e63396' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;,
@@ -7946,7 +7946,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-da03d975-7a09-4e6f-a162-f271d6c71114' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-da03d975-7a09-4e6f-a162-f271d6c71114' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-50c32c8f-749d-4c71-ad7f-55e37b078d1b' class='xr-var-data-in' type='checkbox'><label for='data-50c32c8f-749d-4c71-ad7f-55e37b078d1b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-024af501-9591-416c-8bcf-45191742cc92' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-024af501-9591-416c-8bcf-45191742cc92' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-39ca5fbe-dddc-48d6-9a6b-7c5dc17415dc' class='xr-var-data-in' type='checkbox'><label for='data-39ca5fbe-dddc-48d6-9a6b-7c5dc17415dc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
         True, False, False,  True,  True, False, False, False, False,
         True, False, False,  True, False,  True, False, False, False,
         True,  True,  True, False,  True,  True,  True, False,  True,
@@ -7977,7 +7977,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False,  True, False, False,  True,  True, False, False, False,
         True, False,  True,  True,  True, False,  True,  True, False,
         True, False, False,  True,  True,  True,  True,  True, False,
-       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-033fc3a8-d473-4d61-9f5c-9ff073f43a40' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-033fc3a8-d473-4d61-9f5c-9ff073f43a40' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4985eb93-b241-40a0-a9cf-6ec6bac0f21d' class='xr-var-data-in' type='checkbox'><label for='data-4985eb93-b241-40a0-a9cf-6ec6bac0f21d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
+       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-f95fb043-9878-45c9-a906-5fe0ded0f6ae' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f95fb043-9878-45c9-a906-5fe0ded0f6ae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-24a6766e-cccd-47cf-b749-96edb0f59d53' class='xr-var-data-in' type='checkbox'><label for='data-24a6766e-cccd-47cf-b749-96edb0f59d53' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
        False,  True, False,  True,  True,  True, False, False, False,
        False,  True,  True,  True,  True,  True,  True, False,  True,
         True,  True, False,  True,  True, False,  True, False, False,
@@ -8008,7 +8008,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False, False,  True, False, False,  True,  True, False,  True,
         True, False, False, False, False,  True,  True,  True,  True,
         True,  True,  True, False, False,  True, False, False,  True,
-        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-4d42274e-bb96-42c7-8065-d9d11ba11a30' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4d42274e-bb96-42c7-8065-d9d11ba11a30' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aad12f7f-2e07-4315-a71e-9e69c5ebc78d' class='xr-var-data-in' type='checkbox'><label for='data-aad12f7f-2e07-4315-a71e-9e69c5ebc78d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
+        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-433ae5c4-6802-4b01-9e9b-49a53c023ae8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-433ae5c4-6802-4b01-9e9b-49a53c023ae8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-94057277-7575-4257-8ac3-a6b8753d483b' class='xr-var-data-in' type='checkbox'><label for='data-94057277-7575-4257-8ac3-a6b8753d483b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
        7, 5, 1, 5, 5, 5, 4, 4, 5, 5, 5, 6, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5,
        5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5, 5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4,
        6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5, 4, 4, 5, 8, 3, 4, 4, 4, 7, 5, 4,
@@ -8020,7 +8020,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        4, 5, 3, 5, 6, 5, 4, 3, 8, 2, 4, 4, 6, 8, 4, 3, 4, 3, 2, 5, 6, 6,
        4, 3, 5, 7, 4, 2, 5, 5, 6, 3, 2, 4, 4, 6, 5, 6, 5, 7, 2, 4, 2, 1,
        5, 3, 5, 3, 5, 2, 4, 9, 6, 4, 3, 4, 4, 6, 6, 7, 6, 6, 3, 4, 3, 6,
-       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-55d0bbd0-2deb-4cdd-8c0e-78b243cb8f0f' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-55d0bbd0-2deb-4cdd-8c0e-78b243cb8f0f' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-82074ddf-5402-409b-ad6d-4fc175a25a4c' class='xr-section-summary-in' type='checkbox'  ><label for='section-82074ddf-5402-409b-ad6d-4fc175a25a4c' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-5234c7fd-2061-451b-9121-2390e98e7bb3' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-5234c7fd-2061-451b-9121-2390e98e7bb3' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-fd7fddec-03eb-4f33-b39c-83eb6e51da5e' class='xr-section-summary-in' type='checkbox'  ><label for='section-fd7fddec-03eb-4f33-b39c-83eb6e51da5e' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -8622,7 +8622,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
     PurpleHair                (samples) bool 250B False False ... True True
     CaffeineConsumption       (samples) int64 2kB 4 4 4 3 6 2 2 ... 4 6 4 6 5 5
     sample_dp_mean            (samples) float32 1kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-c6997fb6-e077-47c4-afe9-84fd2571daf1' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c6997fb6-e077-47c4-afe9-84fd2571daf1' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-16961ccf-eca6-4278-a1e3-b0cadd242ea3' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-16961ccf-eca6-4278-a1e3-b0cadd242ea3' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-06bf22f2-17ad-4064-add7-b55dd5ecf75a' class='xr-section-summary-in' type='checkbox'  checked><label for='section-06bf22f2-17ad-4064-add7-b55dd5ecf75a' class='xr-section-summary' >Data variables: <span>(38)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-89798301-661e-4bc5-8193-b8baf56bd975' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-89798301-661e-4bc5-8193-b8baf56bd975' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cb8cc070-694f-4528-a294-ad0e3f180667' class='xr-var-data-in' type='checkbox'><label for='data-cb8cc070-694f-4528-a294-ad0e3f180667' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-fb3c0c64-598f-4677-bb73-c3287e6a4670' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-fb3c0c64-598f-4677-bb73-c3287e6a4670' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-ab6b4103-288d-4bb7-b5b3-71040e8210c0' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-ab6b4103-288d-4bb7-b5b3-71040e8210c0' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-5d975609-e854-4002-9303-cc9eeb047c9e' class='xr-section-summary-in' type='checkbox'  checked><label for='section-5d975609-e854-4002-9303-cc9eeb047c9e' class='xr-section-summary' >Data variables: <span>(38)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-89b43236-88fa-48a1-b2b5-826ec989123b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-89b43236-88fa-48a1-b2b5-826ec989123b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d2ae80aa-8982-4c5f-af1e-e9ce3d121ae0' class='xr-var-data-in' type='checkbox'><label for='data-d2ae80aa-8982-4c5f-af1e-e9ce3d121ae0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8678,7 +8678,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d837fa66-9f23-448d-8214-fc7dfbeebff4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d837fa66-9f23-448d-8214-fc7dfbeebff4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-12b648c9-a661-4213-9559-5c7c089a420b' class='xr-var-data-in' type='checkbox'><label for='data-12b648c9-a661-4213-9559-5c7c089a420b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-768aae2d-d7a7-4b23-9d7c-7912c3dd18dd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-768aae2d-d7a7-4b23-9d7c-7912c3dd18dd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-35adf6a4-acbb-4940-8d54-28bfb801cc7b' class='xr-var-data-in' type='checkbox'><label for='data-35adf6a4-acbb-4940-8d54-28bfb801cc7b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8734,7 +8734,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b838babc-1221-49c0-9fa0-55929d445561' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b838babc-1221-49c0-9fa0-55929d445561' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d48cbd4-40e1-4546-8640-d52d732b64f1' class='xr-var-data-in' type='checkbox'><label for='data-9d48cbd4-40e1-4546-8640-d52d732b64f1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-390f2f0d-20fd-45d4-b29d-8299d190a7b2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-390f2f0d-20fd-45d4-b29d-8299d190a7b2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fa360eb8-a95c-4e35-ba94-47dc9d7cfb24' class='xr-var-data-in' type='checkbox'><label for='data-fa360eb8-a95c-4e35-ba94-47dc9d7cfb24' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8790,7 +8790,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-1ee39025-02d9-472e-8bf0-8a152a001100' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1ee39025-02d9-472e-8bf0-8a152a001100' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e75fd483-ad1a-46b6-8956-c195269c3e0d' class='xr-var-data-in' type='checkbox'><label for='data-e75fd483-ad1a-46b6-8956-c195269c3e0d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-a33aed3f-08c8-4c05-b0f2-0a0a4926a82b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a33aed3f-08c8-4c05-b0f2-0a0a4926a82b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-73d1fe8d-5c80-44f0-afb5-e2f77a969e18' class='xr-var-data-in' type='checkbox'><label for='data-73d1fe8d-5c80-44f0-afb5-e2f77a969e18' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8846,7 +8846,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-4a43e608-fe9d-442c-bf21-10e07e9f8f78' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4a43e608-fe9d-442c-bf21-10e07e9f8f78' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-efeacd17-b926-4db9-b9a4-739bc5316215' class='xr-var-data-in' type='checkbox'><label for='data-efeacd17-b926-4db9-b9a4-739bc5316215' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-9445d79f-9f58-4d5f-8990-c7056e23a6c5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9445d79f-9f58-4d5f-8990-c7056e23a6c5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f2defa3f-09d9-41a1-b0a6-16cd505cc53b' class='xr-var-data-in' type='checkbox'><label for='data-f2defa3f-09d9-41a1-b0a6-16cd505cc53b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8902,7 +8902,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-98c6aa8d-3ff6-4cdb-ae1a-92aa9a0e6c7a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-98c6aa8d-3ff6-4cdb-ae1a-92aa9a0e6c7a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cf84bc88-cde5-4eac-b185-f6e639d48c55' class='xr-var-data-in' type='checkbox'><label for='data-cf84bc88-cde5-4eac-b185-f6e639d48c55' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-cbcee576-0f9c-4f44-b575-7c6a0061003c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cbcee576-0f9c-4f44-b575-7c6a0061003c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-10bcee88-a240-4a5e-86e7-568aadb040fe' class='xr-var-data-in' type='checkbox'><label for='data-10bcee88-a240-4a5e-86e7-568aadb040fe' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8958,7 +8958,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-4077ce1a-94b3-4bc3-ac66-8923f0f89a51' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4077ce1a-94b3-4bc3-ac66-8923f0f89a51' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bcb1906a-a0a4-46c2-8e06-2ced4879536a' class='xr-var-data-in' type='checkbox'><label for='data-bcb1906a-a0a4-46c2-8e06-2ced4879536a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-4d350367-0a7e-4181-8255-c74b04d1e7d8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4d350367-0a7e-4181-8255-c74b04d1e7d8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4ce509a7-39c7-4ea6-94e4-b7a06bc4d82d' class='xr-var-data-in' type='checkbox'><label for='data-4ce509a7-39c7-4ea6-94e4-b7a06bc4d82d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -9015,7 +9015,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-5fd525b8-44c9-4a58-91c9-e89d746ba6ac' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5fd525b8-44c9-4a58-91c9-e89d746ba6ac' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c937ea17-3206-4d0d-ad73-695fb8201561' class='xr-var-data-in' type='checkbox'><label for='data-c937ea17-3206-4d0d-ad73-695fb8201561' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-e00e8b0e-5129-4abe-ae1b-8670f59d0807' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e00e8b0e-5129-4abe-ae1b-8670f59d0807' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ee48721f-b1b3-4037-908e-0bede0802e62' class='xr-var-data-in' type='checkbox'><label for='data-ee48721f-b1b3-4037-908e-0bede0802e62' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9071,7 +9071,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-1af7ab5a-dfca-470e-ad6f-7deecf701e77' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1af7ab5a-dfca-470e-ad6f-7deecf701e77' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-da406961-b663-4692-b141-855612e04914' class='xr-var-data-in' type='checkbox'><label for='data-da406961-b663-4692-b141-855612e04914' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-ee624b4c-cd1e-4896-9ae3-8045d82db10e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ee624b4c-cd1e-4896-9ae3-8045d82db10e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-54557aa0-0c0d-49c4-b67e-682f39d62a08' class='xr-var-data-in' type='checkbox'><label for='data-54557aa0-0c0d-49c4-b67e-682f39d62a08' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9127,7 +9127,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-d593978d-5d11-48f7-9e6f-62aa09625cc5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d593978d-5d11-48f7-9e6f-62aa09625cc5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c3a1b305-1081-426e-b4f2-f9f32cd1c7cc' class='xr-var-data-in' type='checkbox'><label for='data-c3a1b305-1081-426e-b4f2-f9f32cd1c7cc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-71996876-8506-4848-94fe-a9a6f5bd2dbe' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-71996876-8506-4848-94fe-a9a6f5bd2dbe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-07edce1c-5d75-4060-941a-f68ef625856a' class='xr-var-data-in' type='checkbox'><label for='data-07edce1c-5d75-4060-941a-f68ef625856a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9153,7 +9153,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 7 graph layers </td>
+                        <td colspan="2"> 1 chunks in 9 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -9182,7 +9182,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-861d2ab9-c3a2-4d42-b48c-37fbc1045425' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-861d2ab9-c3a2-4d42-b48c-37fbc1045425' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-92c979eb-a274-4902-9e8e-c8e11b7d8f21' class='xr-var-data-in' type='checkbox'><label for='data-92c979eb-a274-4902-9e8e-c8e11b7d8f21' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-5888c152-51ca-4194-b7c4-45ad07636dc7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5888c152-51ca-4194-b7c4-45ad07636dc7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-129b97e2-a80e-4274-97bd-97d17eb759a2' class='xr-var-data-in' type='checkbox'><label for='data-129b97e2-a80e-4274-97bd-97d17eb759a2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9208,7 +9208,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 8 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -9237,7 +9237,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-a948145f-78ad-4273-bd26-115ea9d0a15f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a948145f-78ad-4273-bd26-115ea9d0a15f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-87810c4e-8b07-49ae-9fc7-23bac8348be0' class='xr-var-data-in' type='checkbox'><label for='data-87810c4e-8b07-49ae-9fc7-23bac8348be0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-511a7d46-d381-4ad8-a74a-5aec5492ce1b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-511a7d46-d381-4ad8-a74a-5aec5492ce1b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2c147750-2f0a-42d8-94ed-8256783ff85d' class='xr-var-data-in' type='checkbox'><label for='data-2c147750-2f0a-42d8-94ed-8256783ff85d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9263,7 +9263,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -9292,7 +9292,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-afb1a16f-e17d-4872-a370-f383016a3976' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-afb1a16f-e17d-4872-a370-f383016a3976' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-17aabb4d-d14c-4147-9877-3e333863c6a7' class='xr-var-data-in' type='checkbox'><label for='data-17aabb4d-d14c-4147-9877-3e333863c6a7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-8ef1d7ea-865a-4504-aba9-f103cc5842a6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8ef1d7ea-865a-4504-aba9-f103cc5842a6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2e367522-9d26-40e7-a00b-0595137eefcc' class='xr-var-data-in' type='checkbox'><label for='data-2e367522-9d26-40e7-a00b-0595137eefcc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9318,7 +9318,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -9347,7 +9347,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-daee57a2-7410-4563-86ca-184ee7789e20' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-daee57a2-7410-4563-86ca-184ee7789e20' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-004cc1e2-29af-40ab-b66a-27208b727d09' class='xr-var-data-in' type='checkbox'><label for='data-004cc1e2-29af-40ab-b66a-27208b727d09' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-7f3b55fd-d541-4d89-be15-5d9a03bd66ec' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7f3b55fd-d541-4d89-be15-5d9a03bd66ec' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a4adc012-f280-4a8a-9641-0f78a0361424' class='xr-var-data-in' type='checkbox'><label for='data-a4adc012-f280-4a8a-9641-0f78a0361424' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9373,7 +9373,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -9402,7 +9402,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-68702c31-aed9-4385-b314-7b36f042ca1a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-68702c31-aed9-4385-b314-7b36f042ca1a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7a6a50c7-38a2-48b7-94e6-5761d6bcdc71' class='xr-var-data-in' type='checkbox'><label for='data-7a6a50c7-38a2-48b7-94e6-5761d6bcdc71' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-8855dfbd-aa2f-48fd-b3d1-1e85e4835797' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8855dfbd-aa2f-48fd-b3d1-1e85e4835797' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-59588fb8-e716-4428-9d96-37f9c475994e' class='xr-var-data-in' type='checkbox'><label for='data-59588fb8-e716-4428-9d96-37f9c475994e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9428,7 +9428,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 9 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -9457,7 +9457,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-aecd7e99-0f07-4a38-93e8-ad6eeb20a2b3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-aecd7e99-0f07-4a38-93e8-ad6eeb20a2b3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cecafa97-ee73-4d7b-b406-1f7f82f8655c' class='xr-var-data-in' type='checkbox'><label for='data-cecafa97-ee73-4d7b-b406-1f7f82f8655c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-81e7e7e1-0789-437b-aaae-2dd52955f1ce' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-81e7e7e1-0789-437b-aaae-2dd52955f1ce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d85ff210-5666-43c0-9382-19e2fabb2caa' class='xr-var-data-in' type='checkbox'><label for='data-d85ff210-5666-43c0-9382-19e2fabb2caa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9537,7 +9537,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-9fb5bb32-97fe-475b-8a5d-bdd9ddb8234b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9fb5bb32-97fe-475b-8a5d-bdd9ddb8234b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf3e8385-b3e6-486d-824d-3e67fab6232b' class='xr-var-data-in' type='checkbox'><label for='data-bf3e8385-b3e6-486d-824d-3e67fab6232b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-6d548d4a-2c0e-48f2-9037-fb507a04dda0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6d548d4a-2c0e-48f2-9037-fb507a04dda0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d1b00253-5e9d-4080-8e57-84b7213d137c' class='xr-var-data-in' type='checkbox'><label for='data-d1b00253-5e9d-4080-8e57-84b7213d137c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9593,7 +9593,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-a8537112-660c-46a6-beca-7ff1ba9e3fa5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a8537112-660c-46a6-beca-7ff1ba9e3fa5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3b5a5d6c-75ab-4f4c-897f-7056d6f96163' class='xr-var-data-in' type='checkbox'><label for='data-3b5a5d6c-75ab-4f4c-897f-7056d6f96163' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-9849e5b9-ceca-4daf-a85a-13573f9f368d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9849e5b9-ceca-4daf-a85a-13573f9f368d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c153b0f4-290a-43c4-b50f-dcd23adb74d9' class='xr-var-data-in' type='checkbox'><label for='data-c153b0f4-290a-43c4-b50f-dcd23adb74d9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9649,7 +9649,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-57a95c5f-253c-4a0d-aa03-119bfffea016' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-57a95c5f-253c-4a0d-aa03-119bfffea016' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d694658b-e494-4bbd-84f9-e48b7349c8f3' class='xr-var-data-in' type='checkbox'><label for='data-d694658b-e494-4bbd-84f9-e48b7349c8f3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-5da7b74c-9cdb-43fa-ada0-75d7f6f712c4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5da7b74c-9cdb-43fa-ada0-75d7f6f712c4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b826cfd3-ee47-4f13-bfe5-42bfa5299eca' class='xr-var-data-in' type='checkbox'><label for='data-b826cfd3-ee47-4f13-bfe5-42bfa5299eca' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9729,7 +9729,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-6610eb49-35d7-4dc6-a918-3c7eb4e36f64' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6610eb49-35d7-4dc6-a918-3c7eb4e36f64' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1d6d1d62-4b20-47e6-8f1e-8db8a99805fb' class='xr-var-data-in' type='checkbox'><label for='data-1d6d1d62-4b20-47e6-8f1e-8db8a99805fb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-e529a4a6-0af7-4613-bf5d-ca8bf2815bb4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e529a4a6-0af7-4613-bf5d-ca8bf2815bb4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-86664c8b-722b-4376-b140-63217362f5f4' class='xr-var-data-in' type='checkbox'><label for='data-86664c8b-722b-4376-b140-63217362f5f4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9809,7 +9809,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-a8525083-1518-429f-9f6b-7f8e692c0283' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a8525083-1518-429f-9f6b-7f8e692c0283' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d1800c9e-1ab2-417e-b084-fcda4e74ca10' class='xr-var-data-in' type='checkbox'><label for='data-d1800c9e-1ab2-417e-b084-fcda4e74ca10' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-d0a893a5-dcf0-4cc9-8f1d-ae053f2f6e82' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d0a893a5-dcf0-4cc9-8f1d-ae053f2f6e82' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-41886c6c-4764-4642-9466-c09e20b46c1a' class='xr-var-data-in' type='checkbox'><label for='data-41886c6c-4764-4642-9466-c09e20b46c1a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9865,7 +9865,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-25939ee9-d4b1-4c21-a9ba-e26b3f766f3a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-25939ee9-d4b1-4c21-a9ba-e26b3f766f3a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2a163642-d2dd-4ea2-95ff-29687892d251' class='xr-var-data-in' type='checkbox'><label for='data-2a163642-d2dd-4ea2-95ff-29687892d251' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-52ccfe26-2562-43e1-bf13-10c5f7f2403a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-52ccfe26-2562-43e1-bf13-10c5f7f2403a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-414d77c4-6051-455c-b5e0-d5821980d718' class='xr-var-data-in' type='checkbox'><label for='data-414d77c4-6051-455c-b5e0-d5821980d718' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9920,7 +9920,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-ad5fbed8-27f0-4b41-b063-687d370fedb6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ad5fbed8-27f0-4b41-b063-687d370fedb6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e3ed3d02-3e4f-4c31-aa79-337e2b491c4d' class='xr-var-data-in' type='checkbox'><label for='data-e3ed3d02-3e4f-4c31-aa79-337e2b491c4d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-15ae8e3f-6edd-410f-8537-95e641a0c19e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-15ae8e3f-6edd-410f-8537-95e641a0c19e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8e68990c-3141-464e-8dc7-f7c7b134e3cc' class='xr-var-data-in' type='checkbox'><label for='data-8e68990c-3141-464e-8dc7-f7c7b134e3cc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9975,7 +9975,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-ece48a0c-37fd-44ff-8810-5bcd4c6cd11a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ece48a0c-37fd-44ff-8810-5bcd4c6cd11a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-414e8a7f-436c-4c77-8a84-b48d56a14af9' class='xr-var-data-in' type='checkbox'><label for='data-414e8a7f-436c-4c77-8a84-b48d56a14af9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-806ac9c1-8e6e-48e1-b713-2c4210633cb4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-806ac9c1-8e6e-48e1-b713-2c4210633cb4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b4a6954b-893f-4bbe-9744-eaa150da295e' class='xr-var-data-in' type='checkbox'><label for='data-b4a6954b-893f-4bbe-9744-eaa150da295e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10030,7 +10030,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-a88d9cef-cef7-4e46-ba2d-7675498c83aa' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a88d9cef-cef7-4e46-ba2d-7675498c83aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7b3e9eee-e728-416a-8df2-2490597febe5' class='xr-var-data-in' type='checkbox'><label for='data-7b3e9eee-e728-416a-8df2-2490597febe5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-d0fea9a9-5ec5-4c4a-bd0f-e53506706616' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d0fea9a9-5ec5-4c4a-bd0f-e53506706616' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fab28dea-03aa-4f72-93ad-2d62736690a0' class='xr-var-data-in' type='checkbox'><label for='data-fab28dea-03aa-4f72-93ad-2d62736690a0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10086,7 +10086,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-7db5cadc-3454-4cf2-a395-8b7f94221b9c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7db5cadc-3454-4cf2-a395-8b7f94221b9c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9c6ea309-a3b0-4429-8afd-25297e4a7c6e' class='xr-var-data-in' type='checkbox'><label for='data-9c6ea309-a3b0-4429-8afd-25297e4a7c6e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-7af51115-8028-453b-b723-79fa97023009' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7af51115-8028-453b-b723-79fa97023009' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-048a36aa-6203-45ea-a30f-f31aeeef1e10' class='xr-var-data-in' type='checkbox'><label for='data-048a36aa-6203-45ea-a30f-f31aeeef1e10' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10142,7 +10142,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-aa3e593e-c0a2-4646-9395-24d72bd1fee6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-aa3e593e-c0a2-4646-9395-24d72bd1fee6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8131335c-904a-412a-b133-f3dfa2d59476' class='xr-var-data-in' type='checkbox'><label for='data-8131335c-904a-412a-b133-f3dfa2d59476' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-794fc967-4f57-4fc6-9be7-33e434195fdc' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-794fc967-4f57-4fc6-9be7-33e434195fdc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8e95e404-814d-4aa8-a742-f7c2e23bca3a' class='xr-var-data-in' type='checkbox'><label for='data-8e95e404-814d-4aa8-a742-f7c2e23bca3a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10198,7 +10198,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-1b346347-da1f-4f78-9587-415c61edeefc' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1b346347-da1f-4f78-9587-415c61edeefc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-663b7199-ed73-4ad0-992a-fa7c60da1f21' class='xr-var-data-in' type='checkbox'><label for='data-663b7199-ed73-4ad0-992a-fa7c60da1f21' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-cd2d9422-53b5-42d6-9e4b-2feeb74f1120' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cd2d9422-53b5-42d6-9e4b-2feeb74f1120' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-83eb0321-92b1-4285-9f3d-afd4bedab438' class='xr-var-data-in' type='checkbox'><label for='data-83eb0321-92b1-4285-9f3d-afd4bedab438' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10254,7 +10254,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-4aaddd43-32b9-4400-a94a-68da2b7a95d0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4aaddd43-32b9-4400-a94a-68da2b7a95d0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-24be45d6-c981-42e0-8b28-0d17db3fe060' class='xr-var-data-in' type='checkbox'><label for='data-24be45d6-c981-42e0-8b28-0d17db3fe060' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b99a6f9c-6f1e-4eac-8dd9-1a9acb1fe5a1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b99a6f9c-6f1e-4eac-8dd9-1a9acb1fe5a1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c0ededd-17f3-4b3c-9d40-49a52114c2a5' class='xr-var-data-in' type='checkbox'><label for='data-5c0ededd-17f3-4b3c-9d40-49a52114c2a5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10310,7 +10310,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-10bfb758-a3b4-4ece-94ed-43933173ed8c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-10bfb758-a3b4-4ece-94ed-43933173ed8c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f34c1c2-85b6-4912-a3fe-7feee3faafcd' class='xr-var-data-in' type='checkbox'><label for='data-9f34c1c2-85b6-4912-a3fe-7feee3faafcd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-9ab0efd9-2e20-4501-813b-d95675d228ca' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9ab0efd9-2e20-4501-813b-d95675d228ca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b7ea3966-ed21-4b6f-916c-468656b47e77' class='xr-var-data-in' type='checkbox'><label for='data-b7ea3966-ed21-4b6f-916c-468656b47e77' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10366,7 +10366,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-2ff5e1b9-5e1b-41b5-98b3-545415803b96' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2ff5e1b9-5e1b-41b5-98b3-545415803b96' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8b8dc45f-2b07-481b-80b4-adf6271a2e6e' class='xr-var-data-in' type='checkbox'><label for='data-8b8dc45f-2b07-481b-80b4-adf6271a2e6e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-67f2b9a0-74e0-4c95-bc98-639252eedce5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-67f2b9a0-74e0-4c95-bc98-639252eedce5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2d33e6ef-a3a5-45d4-8352-fcdb1ea1f9be' class='xr-var-data-in' type='checkbox'><label for='data-2d33e6ef-a3a5-45d4-8352-fcdb1ea1f9be' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10422,7 +10422,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-aa80fb77-c138-4158-8588-f2d1b8d6524f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-aa80fb77-c138-4158-8588-f2d1b8d6524f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-abec6111-1549-43bf-ae7b-12c4eaacb780' class='xr-var-data-in' type='checkbox'><label for='data-abec6111-1549-43bf-ae7b-12c4eaacb780' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ab836cb3-102c-4d67-9b7f-ae4f4ff165d5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ab836cb3-102c-4d67-9b7f-ae4f4ff165d5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8420323f-dfd0-4e40-80cb-026764c25309' class='xr-var-data-in' type='checkbox'><label for='data-8420323f-dfd0-4e40-80cb-026764c25309' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10478,7 +10478,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-8bc943ff-0176-43bf-9c85-9399ef26a3bc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8bc943ff-0176-43bf-9c85-9399ef26a3bc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-827abac5-867f-45e1-88a1-a398acce6048' class='xr-var-data-in' type='checkbox'><label for='data-827abac5-867f-45e1-88a1-a398acce6048' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-db658f5d-a9bd-4cc4-a399-b66636910df1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-db658f5d-a9bd-4cc4-a399-b66636910df1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-34662c46-7eb6-4480-95c8-d0563d02c931' class='xr-var-data-in' type='checkbox'><label for='data-34662c46-7eb6-4480-95c8-d0563d02c931' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -10505,7 +10505,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-d6eb443f-a66b-4226-9286-ddb12e83465d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d6eb443f-a66b-4226-9286-ddb12e83465d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ddc48f84-fd76-41a6-8716-77f065667926' class='xr-var-data-in' type='checkbox'><label for='data-ddc48f84-fd76-41a6-8716-77f065667926' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-714d00d9-0adf-4372-8d09-5dcdabebbc36' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-714d00d9-0adf-4372-8d09-5dcdabebbc36' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5ab9b2cd-0ad5-4fc5-a6db-aeec6ecfe2ec' class='xr-var-data-in' type='checkbox'><label for='data-5ab9b2cd-0ad5-4fc5-a6db-aeec6ecfe2ec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -10532,7 +10532,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-7549e641-46bd-4ff9-9ce7-30d9990e6926' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7549e641-46bd-4ff9-9ce7-30d9990e6926' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-55af15d5-3336-42c1-8ade-f7ad4cc99da0' class='xr-var-data-in' type='checkbox'><label for='data-55af15d5-3336-42c1-8ade-f7ad4cc99da0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-66cfedfd-75e3-4b80-8ec3-4997eba762af' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-66cfedfd-75e3-4b80-8ec3-4997eba762af' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6029aa23-d385-48e1-85c4-126806395fb6' class='xr-var-data-in' type='checkbox'><label for='data-6029aa23-d385-48e1-85c4-126806395fb6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -10559,7 +10559,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-f67f8806-7838-4991-ab83-16e4df27a0e0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f67f8806-7838-4991-ab83-16e4df27a0e0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-19c2d13e-9713-4164-8483-43a96bd4de83' class='xr-var-data-in' type='checkbox'><label for='data-19c2d13e-9713-4164-8483-43a96bd4de83' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-31f56a05-57d4-4ccb-8bb9-c3e0356b63a3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-31f56a05-57d4-4ccb-8bb9-c3e0356b63a3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d5563b9e-faac-4037-a87e-0b106197e285' class='xr-var-data-in' type='checkbox'><label for='data-d5563b9e-faac-4037-a87e-0b106197e285' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -10586,7 +10586,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-ea6052e2-13d8-4abb-a3a5-4557a45b9bc6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ea6052e2-13d8-4abb-a3a5-4557a45b9bc6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e9531777-5bce-4582-9a56-67ac54745f88' class='xr-var-data-in' type='checkbox'><label for='data-e9531777-5bce-4582-9a56-67ac54745f88' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-dcbf4232-a181-406b-8513-5cc51e51aed6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dcbf4232-a181-406b-8513-5cc51e51aed6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-90459547-a45a-4c8e-ae6a-de8b389bfc27' class='xr-var-data-in' type='checkbox'><label for='data-90459547-a45a-4c8e-ae6a-de8b389bfc27' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -10597,7 +10597,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-215f10b9-943a-4a67-8146-e9911cd43830' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-215f10b9-943a-4a67-8146-e9911cd43830' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f20afff0-aa4b-4d66-926e-fcb78edacf87' class='xr-var-data-in' type='checkbox'><label for='data-f20afff0-aa4b-4d66-926e-fcb78edacf87' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-54943e38-66c3-418a-b297-3072ec9a009a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-54943e38-66c3-418a-b297-3072ec9a009a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8793d542-8b30-40a4-8235-3bb42e03881d' class='xr-var-data-in' type='checkbox'><label for='data-8793d542-8b30-40a4-8235-3bb42e03881d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10652,7 +10652,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-686badca-75e0-461a-9771-f7285ec878f4' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-686badca-75e0-461a-9771-f7285ec878f4' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-169f473b-00cb-4831-84ff-b27944e8cf33' class='xr-section-summary-in' type='checkbox'  ><label for='section-169f473b-00cb-4831-84ff-b27944e8cf33' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-4ca2f47b-cde4-4270-b1c5-6ae09a4a7fb1' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-4ca2f47b-cde4-4270-b1c5-6ae09a4a7fb1' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-4300dc35-1f6b-4c8c-bcf2-5093bc935ba0' class='xr-section-summary-in' type='checkbox'  ><label for='section-4300dc35-1f6b-4c8c-bcf2-5093bc935ba0' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -11174,7 +11174,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
     PurpleHair                (samples) bool 250B False False ... True True
     CaffeineConsumption       (samples) int64 2kB 4 4 4 3 6 2 2 ... 4 6 4 6 5 5
     sample_dp_mean            (samples) float32 1kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-26b17482-637c-48b7-8483-f21e6adce6a2' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-26b17482-637c-48b7-8483-f21e6adce6a2' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-7308893d-37ee-486c-8edd-ec1f15922805' class='xr-section-summary-in' type='checkbox'  checked><label for='section-7308893d-37ee-486c-8edd-ec1f15922805' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-6c9aa3ee-bca9-4877-be78-1554c401b93b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6c9aa3ee-bca9-4877-be78-1554c401b93b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fb3babaa-4242-4591-a903-3552e0e70318' class='xr-var-data-in' type='checkbox'><label for='data-fb3babaa-4242-4591-a903-3552e0e70318' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-fedbd051-964a-4329-8c13-075baf6d64dc' class='xr-section-summary-in' type='checkbox'  checked><label for='section-fedbd051-964a-4329-8c13-075baf6d64dc' class='xr-section-summary' >Data variables: <span>(41)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-f380c296-0920-444f-9909-98325f53c159' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f380c296-0920-444f-9909-98325f53c159' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-467e7873-d178-45a0-ae0d-0c65eb11e154' class='xr-var-data-in' type='checkbox'><label for='data-467e7873-d178-45a0-ae0d-0c65eb11e154' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-69946215-1d3e-4be3-bf3a-e51fbaf6c34f' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-69946215-1d3e-4be3-bf3a-e51fbaf6c34f' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-405a4ee9-7991-4b5c-b110-0cb1817f0fd3' class='xr-section-summary-in' type='checkbox'  checked><label for='section-405a4ee9-7991-4b5c-b110-0cb1817f0fd3' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-a061324f-08d8-4352-bb57-6d3b6e8df79d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a061324f-08d8-4352-bb57-6d3b6e8df79d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a2607859-e7bb-4930-8774-aff46789cc35' class='xr-var-data-in' type='checkbox'><label for='data-a2607859-e7bb-4930-8774-aff46789cc35' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-817ebf56-2a58-4f95-9d5e-f4c87bfb8973' class='xr-section-summary-in' type='checkbox'  checked><label for='section-817ebf56-2a58-4f95-9d5e-f4c87bfb8973' class='xr-section-summary' >Data variables: <span>(41)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-1c38b668-2d54-4fbc-9ffd-89f89bf96db2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1c38b668-2d54-4fbc-9ffd-89f89bf96db2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d737d4e-c236-4a98-bed1-ec3ee35da9f7' class='xr-var-data-in' type='checkbox'><label for='data-9d737d4e-c236-4a98-bed1-ec3ee35da9f7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11230,7 +11230,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 3), meta=np.ndarray&gt;</div><input id='attrs-bfa80dbe-7e17-495b-ab8f-3f09786705f9' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-bfa80dbe-7e17-495b-ab8f-3f09786705f9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a2491e80-1cf8-428d-93cd-4f4564631985' class='xr-var-data-in' type='checkbox'><label for='data-a2491e80-1cf8-428d-93cd-4f4564631985' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 3), meta=np.ndarray&gt;</div><input id='attrs-d2b1549e-c5c6-49ae-974a-b6812ceb2ce9' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d2b1549e-c5c6-49ae-974a-b6812ceb2ce9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-af590b31-77b6-44d7-8323-1dc61ca91a54' class='xr-var-data-in' type='checkbox'><label for='data-af590b31-77b6-44d7-8323-1dc61ca91a54' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
 Counts are sorted following the ordering defined in the VCF specification.
 
 - For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``
@@ -11294,7 +11294,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-6345b54b-27c2-4494-a9c5-8c6cb98c635f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6345b54b-27c2-4494-a9c5-8c6cb98c635f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-42a198e5-7af5-46e2-bd9c-b9513cb825d7' class='xr-var-data-in' type='checkbox'><label for='data-42a198e5-7af5-46e2-bd9c-b9513cb825d7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-7dde7f24-5263-4a06-9a3c-7e80cb00b88c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7dde7f24-5263-4a06-9a3c-7e80cb00b88c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-45095651-8b11-45ef-96a8-9eb0ada9a39d' class='xr-var-data-in' type='checkbox'><label for='data-45095651-8b11-45ef-96a8-9eb0ada9a39d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
 ploidy and alleles dimensions. The ordering of genotype strings follows the
 ordering outlined in the VCF specification for arrays of size &quot;G&quot;.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -11351,7 +11351,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-1d2d1f2d-a017-4742-a252-56a10ba0615b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1d2d1f2d-a017-4742-a252-56a10ba0615b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d56fc0db-7229-4e04-adff-7d5792214c7e' class='xr-var-data-in' type='checkbox'><label for='data-d56fc0db-7229-4e04-adff-7d5792214c7e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-88a9037e-ec86-49a9-8978-36cbb096c926' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-88a9037e-ec86-49a9-8978-36cbb096c926' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-792b268d-1b94-418f-8efc-f4f334c4231a' class='xr-var-data-in' type='checkbox'><label for='data-792b268d-1b94-418f-8efc-f4f334c4231a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11407,7 +11407,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-f44d0dec-4951-4f89-9026-c54f860e11da' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f44d0dec-4951-4f89-9026-c54f860e11da' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d317ca5-50f2-45fc-a6f1-c1642e297e15' class='xr-var-data-in' type='checkbox'><label for='data-9d317ca5-50f2-45fc-a6f1-c1642e297e15' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-38cceb0d-9e9a-4e73-951f-a611708df4b9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-38cceb0d-9e9a-4e73-951f-a611708df4b9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a7f51966-5de8-46b7-8e9f-6321d0f49d96' class='xr-var-data-in' type='checkbox'><label for='data-a7f51966-5de8-46b7-8e9f-6321d0f49d96' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11463,7 +11463,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-f669097c-82de-446f-b23c-6423d50dc8d5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f669097c-82de-446f-b23c-6423d50dc8d5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8bcf03da-39dd-41ff-a3b8-b98e756ffdeb' class='xr-var-data-in' type='checkbox'><label for='data-8bcf03da-39dd-41ff-a3b8-b98e756ffdeb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-83dbf94b-4524-4cc4-ab61-54a6e3bfb8c6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-83dbf94b-4524-4cc4-ab61-54a6e3bfb8c6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-004c6822-7217-485f-8157-3b3665d9a5aa' class='xr-var-data-in' type='checkbox'><label for='data-004c6822-7217-485f-8157-3b3665d9a5aa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11519,7 +11519,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d1725c90-22c6-48fa-9fd4-d12b8ec52ad4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d1725c90-22c6-48fa-9fd4-d12b8ec52ad4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8452b2f5-ac75-45d2-8d3d-8373da7c669c' class='xr-var-data-in' type='checkbox'><label for='data-8452b2f5-ac75-45d2-8d3d-8373da7c669c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-98a1976d-d3dd-49b2-9ea3-bcf12c2967b0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-98a1976d-d3dd-49b2-9ea3-bcf12c2967b0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6aee80f2-8618-41b8-a8e1-f3201666f972' class='xr-var-data-in' type='checkbox'><label for='data-6aee80f2-8618-41b8-a8e1-f3201666f972' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11575,7 +11575,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-6be5465b-f5ec-4b8c-84e8-fb9c2d0f7141' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6be5465b-f5ec-4b8c-84e8-fb9c2d0f7141' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ae141d64-cd50-405e-a6a1-2a254074f3fd' class='xr-var-data-in' type='checkbox'><label for='data-ae141d64-cd50-405e-a6a1-2a254074f3fd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-f1356e22-df9f-409f-b69e-06729e9e61cf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f1356e22-df9f-409f-b69e-06729e9e61cf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9504cad5-ceb7-42d3-a77b-dec4ca1b08d0' class='xr-var-data-in' type='checkbox'><label for='data-9504cad5-ceb7-42d3-a77b-dec4ca1b08d0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11631,7 +11631,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d609416d-0295-4b4e-82a7-2b8d6e4d4a54' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d609416d-0295-4b4e-82a7-2b8d6e4d4a54' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d095e7d-c455-4b29-a7f0-2d8a27ca3e5d' class='xr-var-data-in' type='checkbox'><label for='data-9d095e7d-c455-4b29-a7f0-2d8a27ca3e5d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ea9b7b4e-c9f5-4e70-8827-39a62f92f019' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ea9b7b4e-c9f5-4e70-8827-39a62f92f019' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a328235f-dbc5-47f7-86e9-048d3e6b6bcb' class='xr-var-data-in' type='checkbox'><label for='data-a328235f-dbc5-47f7-86e9-048d3e6b6bcb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11687,7 +11687,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-275d834b-a426-4336-bac0-72d48baf81dc' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-275d834b-a426-4336-bac0-72d48baf81dc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a238464c-cf35-4a73-8267-7910c0bb7a76' class='xr-var-data-in' type='checkbox'><label for='data-a238464c-cf35-4a73-8267-7910c0bb7a76' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-46e1241c-fb92-445a-ab5e-319abc833fe2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-46e1241c-fb92-445a-ab5e-319abc833fe2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-29e202df-0b6b-4216-937e-7d1c8c8cefe6' class='xr-var-data-in' type='checkbox'><label for='data-29e202df-0b6b-4216-937e-7d1c8c8cefe6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -11744,7 +11744,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-59f0a5b5-294c-433a-b1db-14b23abaca12' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-59f0a5b5-294c-433a-b1db-14b23abaca12' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-35f0b0a9-0a14-476f-a2ca-ee33a2e0260d' class='xr-var-data-in' type='checkbox'><label for='data-35f0b0a9-0a14-476f-a2ca-ee33a2e0260d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-9cf0b257-9ab1-4b0b-b5ed-377cd8e46733' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9cf0b257-9ab1-4b0b-b5ed-377cd8e46733' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-72f86740-22e5-45a4-9a58-a4901958b9cd' class='xr-var-data-in' type='checkbox'><label for='data-72f86740-22e5-45a4-9a58-a4901958b9cd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11800,7 +11800,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-257e7ded-1df6-40da-b8ee-54baa1b99d82' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-257e7ded-1df6-40da-b8ee-54baa1b99d82' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4f820e4f-325f-4d9b-97b6-b084ba7656f5' class='xr-var-data-in' type='checkbox'><label for='data-4f820e4f-325f-4d9b-97b6-b084ba7656f5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-9091f0f4-891c-497d-91c7-a54c1bc06337' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9091f0f4-891c-497d-91c7-a54c1bc06337' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ad7df590-d974-41d6-a988-b7756ab47ef3' class='xr-var-data-in' type='checkbox'><label for='data-ad7df590-d974-41d6-a988-b7756ab47ef3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11856,7 +11856,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-60b627eb-f164-453d-8c18-3cfb2e4c1555' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-60b627eb-f164-453d-8c18-3cfb2e4c1555' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4393463c-9c53-4065-baac-616f31f1875d' class='xr-var-data-in' type='checkbox'><label for='data-4393463c-9c53-4065-baac-616f31f1875d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-2b1b4621-0c02-47dd-9a8d-09d9ded4457e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2b1b4621-0c02-47dd-9a8d-09d9ded4457e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-95b73509-154d-4bb4-8c24-28e06234ea52' class='xr-var-data-in' type='checkbox'><label for='data-95b73509-154d-4bb4-8c24-28e06234ea52' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11882,7 +11882,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 7 graph layers </td>
+                        <td colspan="2"> 1 chunks in 9 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -11911,7 +11911,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6d94caec-3530-4079-ab14-b87096fdf1f6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6d94caec-3530-4079-ab14-b87096fdf1f6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b03dcb8f-0b2d-414e-8f1e-0399ebdf6fbf' class='xr-var-data-in' type='checkbox'><label for='data-b03dcb8f-0b2d-414e-8f1e-0399ebdf6fbf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-3cc9b1e4-5815-4b0e-a295-3e7bedcae31e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3cc9b1e4-5815-4b0e-a295-3e7bedcae31e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e6f15f7f-47a9-45cb-9e6e-7c58d30b80d6' class='xr-var-data-in' type='checkbox'><label for='data-e6f15f7f-47a9-45cb-9e6e-7c58d30b80d6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11937,7 +11937,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 8 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -11966,7 +11966,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-4f7b7cc6-516f-4d31-9aef-3b9adf473d02' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4f7b7cc6-516f-4d31-9aef-3b9adf473d02' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c2541c8-71c1-47d0-89ab-822f8ceb65b9' class='xr-var-data-in' type='checkbox'><label for='data-5c2541c8-71c1-47d0-89ab-822f8ceb65b9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6f2ea5a3-ec16-443b-b3e9-097c6e000996' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6f2ea5a3-ec16-443b-b3e9-097c6e000996' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dbfbcc20-f63f-4293-8273-3400e808b41b' class='xr-var-data-in' type='checkbox'><label for='data-dbfbcc20-f63f-4293-8273-3400e808b41b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11992,7 +11992,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -12021,7 +12021,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-c7208f21-4580-475e-b71a-d478169e19be' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c7208f21-4580-475e-b71a-d478169e19be' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-657a9d5d-e1a9-4dfb-ad08-23b29023912f' class='xr-var-data-in' type='checkbox'><label for='data-657a9d5d-e1a9-4dfb-ad08-23b29023912f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-b583197d-e053-438b-b0f8-6bc8b1bd2b1a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b583197d-e053-438b-b0f8-6bc8b1bd2b1a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-be94d308-8427-4a32-8b1a-f2a7caf0461a' class='xr-var-data-in' type='checkbox'><label for='data-be94d308-8427-4a32-8b1a-f2a7caf0461a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12047,7 +12047,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -12076,7 +12076,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-3c1a719a-81c3-473e-b151-5fb2c57b5f41' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3c1a719a-81c3-473e-b151-5fb2c57b5f41' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c25f6c1d-d683-4572-ae85-b271debc206b' class='xr-var-data-in' type='checkbox'><label for='data-c25f6c1d-d683-4572-ae85-b271debc206b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-925d015b-d55c-4cf6-93b5-da5a7be4713c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-925d015b-d55c-4cf6-93b5-da5a7be4713c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b59208b6-66da-494c-9010-314264abde98' class='xr-var-data-in' type='checkbox'><label for='data-b59208b6-66da-494c-9010-314264abde98' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12102,7 +12102,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -12131,7 +12131,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-881d563a-417b-4c48-9a33-f62106ab9776' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-881d563a-417b-4c48-9a33-f62106ab9776' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e8f3c789-8232-49c4-a9fe-967fff4cfb08' class='xr-var-data-in' type='checkbox'><label for='data-e8f3c789-8232-49c4-a9fe-967fff4cfb08' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-b7082139-7b05-4a76-82d6-ea3886b6dbe2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b7082139-7b05-4a76-82d6-ea3886b6dbe2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f910831-2abc-4cf1-85b8-b55c36b125d3' class='xr-var-data-in' type='checkbox'><label for='data-9f910831-2abc-4cf1-85b8-b55c36b125d3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12157,7 +12157,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 9 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -12186,7 +12186,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-688a7dbf-68bb-48b8-9b54-ffc535c6f97e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-688a7dbf-68bb-48b8-9b54-ffc535c6f97e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8990ba57-a941-4020-91f1-eda98fcde120' class='xr-var-data-in' type='checkbox'><label for='data-8990ba57-a941-4020-91f1-eda98fcde120' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-b8e97956-1a81-45a0-9893-e4bbadc68222' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b8e97956-1a81-45a0-9893-e4bbadc68222' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b853f324-f67a-4dd3-bc4c-c8e41d26a7b8' class='xr-var-data-in' type='checkbox'><label for='data-b853f324-f67a-4dd3-bc4c-c8e41d26a7b8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12266,7 +12266,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-c571745a-96fa-4650-8c09-fe0946b03afc' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c571745a-96fa-4650-8c09-fe0946b03afc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c7fc8569-fa00-4423-b2ea-85712ac9406a' class='xr-var-data-in' type='checkbox'><label for='data-c7fc8569-fa00-4423-b2ea-85712ac9406a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-c5deef6e-87d7-4577-a5be-3cd700c244cf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c5deef6e-87d7-4577-a5be-3cd700c244cf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6ca265ef-a7c3-4196-a88f-d5990e13fc5c' class='xr-var-data-in' type='checkbox'><label for='data-6ca265ef-a7c3-4196-a88f-d5990e13fc5c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12322,7 +12322,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-7efe23fd-c470-4b47-a9b4-0385057fa53f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7efe23fd-c470-4b47-a9b4-0385057fa53f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-de5a4bf2-6c11-4837-b791-d49d0d1605a2' class='xr-var-data-in' type='checkbox'><label for='data-de5a4bf2-6c11-4837-b791-d49d0d1605a2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-82c1a408-fc34-4b32-8edc-2aa2034b08d0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-82c1a408-fc34-4b32-8edc-2aa2034b08d0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0fd0f704-e94b-4fb3-93c5-1b4a2ff70595' class='xr-var-data-in' type='checkbox'><label for='data-0fd0f704-e94b-4fb3-93c5-1b4a2ff70595' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12378,7 +12378,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-d54397b1-e3e4-4a74-9033-3e5828bae4a4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d54397b1-e3e4-4a74-9033-3e5828bae4a4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a95a1754-8af5-4334-a8c3-910a9bc55167' class='xr-var-data-in' type='checkbox'><label for='data-a95a1754-8af5-4334-a8c3-910a9bc55167' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-e196fe00-8cbe-4808-bc21-fc9d6225cbd1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e196fe00-8cbe-4808-bc21-fc9d6225cbd1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2125d4b8-b677-4d39-98a8-63a059539146' class='xr-var-data-in' type='checkbox'><label for='data-2125d4b8-b677-4d39-98a8-63a059539146' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12458,7 +12458,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-c8ad7e3e-c0dc-4cfc-8375-d7d995361213' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c8ad7e3e-c0dc-4cfc-8375-d7d995361213' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-967bf55f-c2b6-4dfd-9493-3d8a6d7c6885' class='xr-var-data-in' type='checkbox'><label for='data-967bf55f-c2b6-4dfd-9493-3d8a6d7c6885' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-8197e345-894d-458d-a75f-4c2c4db5e0d7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8197e345-894d-458d-a75f-4c2c4db5e0d7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-82e95c11-40eb-4d5c-96e8-8e228e3ea8b0' class='xr-var-data-in' type='checkbox'><label for='data-82e95c11-40eb-4d5c-96e8-8e228e3ea8b0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12538,7 +12538,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-3795078d-4ee3-49dd-80de-2b7a3715f062' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3795078d-4ee3-49dd-80de-2b7a3715f062' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c297b7e-333c-4b91-984f-e602ae207f11' class='xr-var-data-in' type='checkbox'><label for='data-5c297b7e-333c-4b91-984f-e602ae207f11' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-16cccab9-324d-4ac0-b5a2-63f61a6ff152' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-16cccab9-324d-4ac0-b5a2-63f61a6ff152' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e9c30202-7032-4c86-84c2-01dade9cbb34' class='xr-var-data-in' type='checkbox'><label for='data-e9c30202-7032-4c86-84c2-01dade9cbb34' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12594,7 +12594,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-a3af7291-1f86-47b8-aecf-f5d70d3ae02c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a3af7291-1f86-47b8-aecf-f5d70d3ae02c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-145bd0be-270c-41ed-8d3b-c712148885f2' class='xr-var-data-in' type='checkbox'><label for='data-145bd0be-270c-41ed-8d3b-c712148885f2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-83912046-662b-4c01-b8d9-06677dc6894e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-83912046-662b-4c01-b8d9-06677dc6894e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fec28d67-af7b-4777-9947-4247f598b80c' class='xr-var-data-in' type='checkbox'><label for='data-fec28d67-af7b-4777-9947-4247f598b80c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12649,7 +12649,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-e4d7528e-c812-4ab0-bc23-7f5f817e678e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e4d7528e-c812-4ab0-bc23-7f5f817e678e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a185023c-6d61-4228-9f50-7bf1b0ae11c6' class='xr-var-data-in' type='checkbox'><label for='data-a185023c-6d61-4228-9f50-7bf1b0ae11c6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-ddee6622-c484-4697-9a38-82c4f11a30ea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ddee6622-c484-4697-9a38-82c4f11a30ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-343dbdb5-9e1f-4336-be02-a9a034a0bee8' class='xr-var-data-in' type='checkbox'><label for='data-343dbdb5-9e1f-4336-be02-a9a034a0bee8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12704,7 +12704,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-d9773231-e1a8-4176-9c9d-abb05511e312' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d9773231-e1a8-4176-9c9d-abb05511e312' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f73ca544-d891-45b4-9c07-10a572bb05be' class='xr-var-data-in' type='checkbox'><label for='data-f73ca544-d891-45b4-9c07-10a572bb05be' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-01506156-65c5-41c4-8ac6-fa7945f3d7f0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-01506156-65c5-41c4-8ac6-fa7945f3d7f0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4f2d7a22-cecd-4aa6-93e2-b7b4ec2259a7' class='xr-var-data-in' type='checkbox'><label for='data-4f2d7a22-cecd-4aa6-93e2-b7b4ec2259a7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12759,7 +12759,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-4e30ed43-a269-4826-9d18-ffb4915da0e1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4e30ed43-a269-4826-9d18-ffb4915da0e1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1bf26d5b-4b5b-4ffe-aec5-c71bc9345d62' class='xr-var-data-in' type='checkbox'><label for='data-1bf26d5b-4b5b-4ffe-aec5-c71bc9345d62' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-6d733657-cbfb-44a8-8660-35d2563b115e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6d733657-cbfb-44a8-8660-35d2563b115e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-974f31c8-a97e-478b-964b-a478086378c6' class='xr-var-data-in' type='checkbox'><label for='data-974f31c8-a97e-478b-964b-a478086378c6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12815,7 +12815,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-0167753f-a7f0-446f-a931-e50a520facbd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0167753f-a7f0-446f-a931-e50a520facbd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-00088b78-983b-456e-8c67-66e5e86ac15c' class='xr-var-data-in' type='checkbox'><label for='data-00088b78-983b-456e-8c67-66e5e86ac15c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b6b2fd6f-277b-4c81-bb82-8396930dfe21' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b6b2fd6f-277b-4c81-bb82-8396930dfe21' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-17305bb5-eb78-4890-9051-74386afa437d' class='xr-var-data-in' type='checkbox'><label for='data-17305bb5-eb78-4890-9051-74386afa437d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12871,7 +12871,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-1df72500-1b9b-4a27-9b42-1d9349ae624f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1df72500-1b9b-4a27-9b42-1d9349ae624f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-531a37a7-135f-439b-9468-bc10a049362f' class='xr-var-data-in' type='checkbox'><label for='data-531a37a7-135f-439b-9468-bc10a049362f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-ea8a9ac8-45fa-4860-bba7-842a9db76804' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ea8a9ac8-45fa-4860-bba7-842a9db76804' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c6fb60ed-2b22-4fa1-b5ab-0f0da6f57df2' class='xr-var-data-in' type='checkbox'><label for='data-c6fb60ed-2b22-4fa1-b5ab-0f0da6f57df2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12927,7 +12927,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-7ddd7ee4-410f-443c-9871-e1a339f2209a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7ddd7ee4-410f-443c-9871-e1a339f2209a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0abb9e6f-1161-404a-9bcd-1185a9b10acb' class='xr-var-data-in' type='checkbox'><label for='data-0abb9e6f-1161-404a-9bcd-1185a9b10acb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-462dae04-9314-454d-acb7-282e2677e843' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-462dae04-9314-454d-acb7-282e2677e843' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fd49ec4a-f029-4ec4-aeec-d7dda17061e4' class='xr-var-data-in' type='checkbox'><label for='data-fd49ec4a-f029-4ec4-aeec-d7dda17061e4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12983,7 +12983,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-bbc1179b-30cf-45df-b8bc-1609f1c5f1bf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-bbc1179b-30cf-45df-b8bc-1609f1c5f1bf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d4bc7d16-ed02-4425-ae19-cd7d5e33352b' class='xr-var-data-in' type='checkbox'><label for='data-d4bc7d16-ed02-4425-ae19-cd7d5e33352b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-589cb5fa-25d0-4bfe-bb47-69ef2a72a48f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-589cb5fa-25d0-4bfe-bb47-69ef2a72a48f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-09129e9d-7a5a-4d7f-b3e3-e2659b164fb5' class='xr-var-data-in' type='checkbox'><label for='data-09129e9d-7a5a-4d7f-b3e3-e2659b164fb5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13039,7 +13039,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-c0d603d2-b485-46ed-99ad-936fb2f2176a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c0d603d2-b485-46ed-99ad-936fb2f2176a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-03f6eb55-a9cd-43d6-9edc-64044ae08cb9' class='xr-var-data-in' type='checkbox'><label for='data-03f6eb55-a9cd-43d6-9edc-64044ae08cb9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-cf3fb720-7092-481c-922e-3f19c6d8adf9' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cf3fb720-7092-481c-922e-3f19c6d8adf9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-43345bdd-9ff5-435b-9372-6dd2a5729f03' class='xr-var-data-in' type='checkbox'><label for='data-43345bdd-9ff5-435b-9372-6dd2a5729f03' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13095,7 +13095,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-0c1be425-b010-4694-be02-b51c18a761d0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0c1be425-b010-4694-be02-b51c18a761d0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-245d18d8-450d-47f6-9e2f-bcd39b05f8fc' class='xr-var-data-in' type='checkbox'><label for='data-245d18d8-450d-47f6-9e2f-bcd39b05f8fc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-2a82d5a4-0271-425e-9fdb-31603c261532' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2a82d5a4-0271-425e-9fdb-31603c261532' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-613cd43c-e9da-4943-b978-d918787b05b1' class='xr-var-data-in' type='checkbox'><label for='data-613cd43c-e9da-4943-b978-d918787b05b1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13151,7 +13151,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-7853a277-a9e2-4e38-bf76-7db411b0ce2b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7853a277-a9e2-4e38-bf76-7db411b0ce2b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b641a9e7-dc40-4508-9162-e9438382765e' class='xr-var-data-in' type='checkbox'><label for='data-b641a9e7-dc40-4508-9162-e9438382765e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-60a1ab7a-0b04-4b45-902c-c2c6c617a283' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-60a1ab7a-0b04-4b45-902c-c2c6c617a283' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0fb153f4-3461-493d-b4ba-9ca14bb439b7' class='xr-var-data-in' type='checkbox'><label for='data-0fb153f4-3461-493d-b4ba-9ca14bb439b7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13207,7 +13207,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-3c69980e-811c-486c-8dc0-33c08b4c0708' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3c69980e-811c-486c-8dc0-33c08b4c0708' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a52a0b05-7037-4dbe-a5ce-f25bf46c98cc' class='xr-var-data-in' type='checkbox'><label for='data-a52a0b05-7037-4dbe-a5ce-f25bf46c98cc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-92a0cae2-178d-4477-bc65-785f71367d83' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-92a0cae2-178d-4477-bc65-785f71367d83' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-66ae0c49-d1e8-4550-a9c1-c388a52cbb5a' class='xr-var-data-in' type='checkbox'><label for='data-66ae0c49-d1e8-4550-a9c1-c388a52cbb5a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -13234,7 +13234,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-78fd0ead-236e-48d0-a41e-4e42440a0e4f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-78fd0ead-236e-48d0-a41e-4e42440a0e4f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ced48717-396f-474e-b0a6-b8765ec1b433' class='xr-var-data-in' type='checkbox'><label for='data-ced48717-396f-474e-b0a6-b8765ec1b433' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-46b61a9c-60c1-4ec7-bba9-d132158ec94c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-46b61a9c-60c1-4ec7-bba9-d132158ec94c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e40a8eb0-3fc3-45fc-8318-d0c0d7f50afd' class='xr-var-data-in' type='checkbox'><label for='data-e40a8eb0-3fc3-45fc-8318-d0c0d7f50afd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -13261,7 +13261,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-a0ab223f-124d-4fe0-af4b-17a0a51613aa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a0ab223f-124d-4fe0-af4b-17a0a51613aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ae4ac1b0-6d28-4fa9-a333-6447cf15c480' class='xr-var-data-in' type='checkbox'><label for='data-ae4ac1b0-6d28-4fa9-a333-6447cf15c480' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-5dc78928-a0ed-48ac-9667-1fc35759787a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5dc78928-a0ed-48ac-9667-1fc35759787a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d131fae-17a8-46ca-a3b8-70b06ac1b1f7' class='xr-var-data-in' type='checkbox'><label for='data-9d131fae-17a8-46ca-a3b8-70b06ac1b1f7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -13288,7 +13288,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-5c6adaeb-05e8-4558-8a84-00e8c25bdb28' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5c6adaeb-05e8-4558-8a84-00e8c25bdb28' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c4794d5d-0b55-4fb6-9451-8fb11d663e8b' class='xr-var-data-in' type='checkbox'><label for='data-c4794d5d-0b55-4fb6-9451-8fb11d663e8b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-bf8b1ef1-0ed2-422d-91ee-673e0d104314' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bf8b1ef1-0ed2-422d-91ee-673e0d104314' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-da064c5e-6a47-4638-ac77-f565006f85c6' class='xr-var-data-in' type='checkbox'><label for='data-da064c5e-6a47-4638-ac77-f565006f85c6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -13315,7 +13315,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-2f4bf66a-ca35-4a7c-93c4-f95918444e29' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2f4bf66a-ca35-4a7c-93c4-f95918444e29' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d34412f-a575-4fff-a79c-133c2a9b0132' class='xr-var-data-in' type='checkbox'><label for='data-9d34412f-a575-4fff-a79c-133c2a9b0132' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-49d631f4-5eeb-44fd-ac27-8445f64ad20b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-49d631f4-5eeb-44fd-ac27-8445f64ad20b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f331b30e-495c-4f56-ad5f-4a17d02a75a9' class='xr-var-data-in' type='checkbox'><label for='data-f331b30e-495c-4f56-ad5f-4a17d02a75a9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -13326,7 +13326,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6e1c545f-98c2-4661-80db-d2b9c5e9a4b5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6e1c545f-98c2-4661-80db-d2b9c5e9a4b5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4fa203d7-d575-4104-bbaa-38eae0a12983' class='xr-var-data-in' type='checkbox'><label for='data-4fa203d7-d575-4104-bbaa-38eae0a12983' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-27e2e019-9030-49b6-ac33-a6ad7d0a25a7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-27e2e019-9030-49b6-ac33-a6ad7d0a25a7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d10b7299-e154-4869-8566-bc81e30fa04d' class='xr-var-data-in' type='checkbox'><label for='data-d10b7299-e154-4869-8566-bc81e30fa04d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13381,7 +13381,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-168d8aa7-5824-46cb-b797-e1ea5d68011f' class='xr-section-summary-in' type='checkbox'  ><label for='section-168d8aa7-5824-46cb-b797-e1ea5d68011f' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-1387227c-6581-4b97-9095-d0cc79428069' class='xr-index-data-in' type='checkbox'/><label for='index-1387227c-6581-4b97-9095-d0cc79428069' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-c0b6e218-fdc8-4cb6-aa2a-9dac3c464565' class='xr-section-summary-in' type='checkbox'  ><label for='section-c0b6e218-fdc8-4cb6-aa2a-9dac3c464565' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-29ba557b-5459-47fc-b73e-1a6ab8216fe4' class='xr-section-summary-in' type='checkbox'  ><label for='section-29ba557b-5459-47fc-b73e-1a6ab8216fe4' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-9d744616-f4e7-44de-a087-13ea456fb353' class='xr-index-data-in' type='checkbox'/><label for='index-9d744616-f4e7-44de-a087-13ea456fb353' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-9a39b4ed-73f8-4111-b267-1dd53e3f7004' class='xr-section-summary-in' type='checkbox'  ><label for='section-9a39b4ed-73f8-4111-b267-1dd53e3f7004' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -13916,7 +13916,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
     CaffeineConsumption       (samples) int64 2kB 4 4 4 3 6 2 2 ... 4 6 4 6 5 5
     sample_dp_mean            (samples) float32 1kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
     call_dosage               (variants, samples) int64 17MB dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-3ec407ce-10b2-40bc-98c0-24ca45411bb5' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-3ec407ce-10b2-40bc-98c0-24ca45411bb5' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 8394</li><li><span>traits</span>: 1</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-973d144b-5b11-4749-8e06-089dbe5deba2' class='xr-section-summary-in' type='checkbox'  checked><label for='section-973d144b-5b11-4749-8e06-089dbe5deba2' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-aa1a70b1-b67c-4b89-8c39-ddb25cea7b96' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-aa1a70b1-b67c-4b89-8c39-ddb25cea7b96' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5403d96f-2be1-4a44-ba95-54125ee03be6' class='xr-var-data-in' type='checkbox'><label for='data-5403d96f-2be1-4a44-ba95-54125ee03be6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-291e1029-79ae-4bdf-901e-e394f5b6f714' class='xr-section-summary-in' type='checkbox'  checked><label for='section-291e1029-79ae-4bdf-901e-e394f5b6f714' class='xr-section-summary' >Data variables: <span>(45)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_beta</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-16ce1859-fad4-4c1e-99cd-957834a32e2f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-16ce1859-fad4-4c1e-99cd-957834a32e2f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ee15bd12-34be-4884-b505-ae6698f983e1' class='xr-var-data-in' type='checkbox'><label for='data-ee15bd12-34be-4884-b505-ae6698f983e1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Beta values associated with each variant and trait.</dd></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-65f0b56d-cea4-4a7a-a3d7-13fe8f35e10c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-65f0b56d-cea4-4a7a-a3d7-13fe8f35e10c' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 8394</li><li><span>traits</span>: 1</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-f3b61590-b9e3-43e2-9bed-eaed3600b4ba' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f3b61590-b9e3-43e2-9bed-eaed3600b4ba' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-85d09cb2-763c-47af-b40d-800b3c63ba1c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-85d09cb2-763c-47af-b40d-800b3c63ba1c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-09abf17c-0bac-419f-ae95-bf4b3ff6d6d2' class='xr-var-data-in' type='checkbox'><label for='data-09abf17c-0bac-419f-ae95-bf4b3ff6d6d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a66b0495-8543-4020-87e5-74d75c14a211' class='xr-section-summary-in' type='checkbox'  checked><label for='section-a66b0495-8543-4020-87e5-74d75c14a211' class='xr-section-summary' >Data variables: <span>(45)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_beta</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-8153e842-1d21-48e0-89b3-da70c35072d2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8153e842-1d21-48e0-89b3-da70c35072d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6ef02f3b-f57f-40fe-ace4-b6027133b8ef' class='xr-var-data-in' type='checkbox'><label for='data-6ef02f3b-f57f-40fe-ace4-b6027133b8ef' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Beta values associated with each variant and trait.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13972,7 +13972,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_t_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-ee289589-d4d4-43f0-ac2b-91b367a5b738' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ee289589-d4d4-43f0-ac2b-91b367a5b738' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3aa28948-0999-4ca5-acc3-f44c5f37f79b' class='xr-var-data-in' type='checkbox'><label for='data-3aa28948-0999-4ca5-acc3-f44c5f37f79b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>T statistics for each beta.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_t_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-9c1d186e-2c43-431e-a7c4-c84073e7eaec' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9c1d186e-2c43-431e-a7c4-c84073e7eaec' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1acbd456-acb9-477d-929f-9a046700fff6' class='xr-var-data-in' type='checkbox'><label for='data-1acbd456-acb9-477d-929f-9a046700fff6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>T statistics for each beta.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14028,7 +14028,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_p_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-9c33f00f-e8db-45a8-b1cd-b17ac77537cf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9c33f00f-e8db-45a8-b1cd-b17ac77537cf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7b9aa7b6-22ba-4af0-9539-37d0ec7e3585' class='xr-var-data-in' type='checkbox'><label for='data-7b9aa7b6-22ba-4af0-9539-37d0ec7e3585' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_p_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-f061a53e-f405-4920-a327-5c6c5b95b7d0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f061a53e-f405-4920-a327-5c6c5b95b7d0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0db7a238-9b64-4f09-80a0-297c605baee5' class='xr-var-data-in' type='checkbox'><label for='data-0db7a238-9b64-4f09-80a0-297c605baee5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14084,7 +14084,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-0019f095-c1c6-4ae6-8da7-fd658228700c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0019f095-c1c6-4ae6-8da7-fd658228700c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7cb7f60d-b468-4ce5-902e-d7284410f507' class='xr-var-data-in' type='checkbox'><label for='data-7cb7f60d-b468-4ce5-902e-d7284410f507' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-5de87c6d-2571-4c19-9f0a-676766bc4e37' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5de87c6d-2571-4c19-9f0a-676766bc4e37' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d51bf6fe-2a5f-4e77-9e99-9d4dc5ad0499' class='xr-var-data-in' type='checkbox'><label for='data-d51bf6fe-2a5f-4e77-9e99-9d4dc5ad0499' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14140,7 +14140,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 3), meta=np.ndarray&gt;</div><input id='attrs-1d75a7d6-8a5b-4bb0-8819-44d20bc659ce' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1d75a7d6-8a5b-4bb0-8819-44d20bc659ce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a1902724-ce7d-4fe2-86f4-f24b37f313ca' class='xr-var-data-in' type='checkbox'><label for='data-a1902724-ce7d-4fe2-86f4-f24b37f313ca' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 3), meta=np.ndarray&gt;</div><input id='attrs-deca0555-a396-4044-9173-c71e19d438c1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-deca0555-a396-4044-9173-c71e19d438c1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f974741f-eff0-4ec3-be42-d68d0eda838d' class='xr-var-data-in' type='checkbox'><label for='data-f974741f-eff0-4ec3-be42-d68d0eda838d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
 Counts are sorted following the ordering defined in the VCF specification.
 
 - For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``
@@ -14204,7 +14204,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-c76b2a7c-9d7a-4cb2-93f4-b249ee87dd52' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c76b2a7c-9d7a-4cb2-93f4-b249ee87dd52' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-368cdf98-777a-4e70-9778-494ecb673cd2' class='xr-var-data-in' type='checkbox'><label for='data-368cdf98-777a-4e70-9778-494ecb673cd2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-299e4296-c37d-4ad1-b447-f1ba144c37f5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-299e4296-c37d-4ad1-b447-f1ba144c37f5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-17858826-bcac-49f1-b150-8f40dd116185' class='xr-var-data-in' type='checkbox'><label for='data-17858826-bcac-49f1-b150-8f40dd116185' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
 ploidy and alleles dimensions. The ordering of genotype strings follows the
 ordering outlined in the VCF specification for arrays of size &quot;G&quot;.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -14261,7 +14261,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-44cf1be2-ef06-41a4-9833-aa8d2a92f565' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-44cf1be2-ef06-41a4-9833-aa8d2a92f565' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2b53a50b-4f8e-434b-b157-2ac35d802154' class='xr-var-data-in' type='checkbox'><label for='data-2b53a50b-4f8e-434b-b157-2ac35d802154' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-1eb5088b-b95c-4aeb-9e23-f390f0658956' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1eb5088b-b95c-4aeb-9e23-f390f0658956' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2e3528c3-b216-4728-bb17-fdd1aeef8a87' class='xr-var-data-in' type='checkbox'><label for='data-2e3528c3-b216-4728-bb17-fdd1aeef8a87' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14317,7 +14317,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-e7328bf4-d29e-44c9-88df-fcafcb95f2fc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e7328bf4-d29e-44c9-88df-fcafcb95f2fc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e0603465-9538-4e0c-b7bb-06231b7ee0eb' class='xr-var-data-in' type='checkbox'><label for='data-e0603465-9538-4e0c-b7bb-06231b7ee0eb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-48910a06-1bc1-4a0b-92af-c210a6eca962' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-48910a06-1bc1-4a0b-92af-c210a6eca962' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f723d58-6847-4580-a9a7-9740fc730538' class='xr-var-data-in' type='checkbox'><label for='data-9f723d58-6847-4580-a9a7-9740fc730538' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14373,7 +14373,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-31d36988-d75a-473d-95d8-af11cbf09a12' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-31d36988-d75a-473d-95d8-af11cbf09a12' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d28cfad5-4cf4-46b4-b04b-45e58fcaae4b' class='xr-var-data-in' type='checkbox'><label for='data-d28cfad5-4cf4-46b4-b04b-45e58fcaae4b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-91587130-2c93-4665-9394-9a5545a5aee1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-91587130-2c93-4665-9394-9a5545a5aee1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b4ad3b03-a80a-4477-bfc5-2b4e49692b27' class='xr-var-data-in' type='checkbox'><label for='data-b4ad3b03-a80a-4477-bfc5-2b4e49692b27' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14429,7 +14429,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-bbea4550-a56f-4de5-a5fb-7de36dfbbda8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bbea4550-a56f-4de5-a5fb-7de36dfbbda8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-56340f33-c140-4fd4-a1bc-6d6f654a51c9' class='xr-var-data-in' type='checkbox'><label for='data-56340f33-c140-4fd4-a1bc-6d6f654a51c9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-443f9f4a-2e9e-4c3e-a346-3e723c592db9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-443f9f4a-2e9e-4c3e-a346-3e723c592db9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-10bcbfaf-1455-416e-8808-8e612921549f' class='xr-var-data-in' type='checkbox'><label for='data-10bcbfaf-1455-416e-8808-8e612921549f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14485,7 +14485,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-91dd519a-507b-4300-be15-aa61895af560' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-91dd519a-507b-4300-be15-aa61895af560' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9ee1f80e-1432-451b-8477-cb1ba7c70996' class='xr-var-data-in' type='checkbox'><label for='data-9ee1f80e-1432-451b-8477-cb1ba7c70996' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-b974cce4-b46c-491d-8dc4-1416388b92d7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b974cce4-b46c-491d-8dc4-1416388b92d7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-212f7b3e-7a57-4af4-a1e5-05880882dfdc' class='xr-var-data-in' type='checkbox'><label for='data-212f7b3e-7a57-4af4-a1e5-05880882dfdc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14541,7 +14541,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-aea7506e-7e1d-4051-884c-393bbbaa385f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-aea7506e-7e1d-4051-884c-393bbbaa385f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-76185f16-21b3-40bd-8cc3-3422c7d32632' class='xr-var-data-in' type='checkbox'><label for='data-76185f16-21b3-40bd-8cc3-3422c7d32632' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-60b81e2d-2c47-466f-8402-aad59809d132' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-60b81e2d-2c47-466f-8402-aad59809d132' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c8968584-2830-4383-b908-3906cb73db4b' class='xr-var-data-in' type='checkbox'><label for='data-c8968584-2830-4383-b908-3906cb73db4b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14597,7 +14597,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-07241ed4-bc09-4456-bebf-18bfac2a9942' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-07241ed4-bc09-4456-bebf-18bfac2a9942' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-93de1b99-cd0d-4373-9156-dd1b72233687' class='xr-var-data-in' type='checkbox'><label for='data-93de1b99-cd0d-4373-9156-dd1b72233687' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-6234a6e5-123f-4a21-90d1-126f061a83aa' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6234a6e5-123f-4a21-90d1-126f061a83aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ff96c13b-ccc2-46d0-8339-00badff43945' class='xr-var-data-in' type='checkbox'><label for='data-ff96c13b-ccc2-46d0-8339-00badff43945' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -14654,7 +14654,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-8f22e1b7-be3f-4fb9-b336-2726235faa62' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8f22e1b7-be3f-4fb9-b336-2726235faa62' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-188ad1b7-637e-4bd2-8ffa-3be9969b0d78' class='xr-var-data-in' type='checkbox'><label for='data-188ad1b7-637e-4bd2-8ffa-3be9969b0d78' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-7523c784-bf1c-42b2-b41c-dccb10a3fde5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7523c784-bf1c-42b2-b41c-dccb10a3fde5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d59fe7dc-692f-45fe-8abf-9fa1eab115ca' class='xr-var-data-in' type='checkbox'><label for='data-d59fe7dc-692f-45fe-8abf-9fa1eab115ca' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14710,7 +14710,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-dc6c6537-32dd-4dc7-9edf-33ef17889230' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dc6c6537-32dd-4dc7-9edf-33ef17889230' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9c1c7753-77d2-4f51-9160-af0dfa7444d2' class='xr-var-data-in' type='checkbox'><label for='data-9c1c7753-77d2-4f51-9160-af0dfa7444d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-c779cfb9-6730-4418-9c18-b1245487c0f9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c779cfb9-6730-4418-9c18-b1245487c0f9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b56ea90b-65cf-40a6-a6a6-3cfc471d96c6' class='xr-var-data-in' type='checkbox'><label for='data-b56ea90b-65cf-40a6-a6a6-3cfc471d96c6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14766,7 +14766,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-fb45a14c-f028-431c-8823-846b5e32bd14' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb45a14c-f028-431c-8823-846b5e32bd14' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf5da40b-8a69-4458-8cbb-6daa39326f77' class='xr-var-data-in' type='checkbox'><label for='data-bf5da40b-8a69-4458-8cbb-6daa39326f77' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-a7f7d6a7-ab0c-44c0-985e-08b380f17cc9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a7f7d6a7-ab0c-44c0-985e-08b380f17cc9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e3ea12a2-6dac-4dc7-99b7-09375bef3cac' class='xr-var-data-in' type='checkbox'><label for='data-e3ea12a2-6dac-4dc7-99b7-09375bef3cac' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14792,7 +14792,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 7 graph layers </td>
+                        <td colspan="2"> 1 chunks in 9 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -14821,7 +14821,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-58ed9bb9-356d-4bd2-ad3b-7f683bb6f6e1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-58ed9bb9-356d-4bd2-ad3b-7f683bb6f6e1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8499e5dc-f349-4e4a-b050-760dfb26d393' class='xr-var-data-in' type='checkbox'><label for='data-8499e5dc-f349-4e4a-b050-760dfb26d393' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-667d82e7-a368-4e5a-a038-404b3992cf1b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-667d82e7-a368-4e5a-a038-404b3992cf1b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5d43d641-7400-4fc1-8e7e-be0037685127' class='xr-var-data-in' type='checkbox'><label for='data-5d43d641-7400-4fc1-8e7e-be0037685127' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14847,7 +14847,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 8 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -14876,7 +14876,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-f9233588-d660-4ced-a543-0656f0a01209' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f9233588-d660-4ced-a543-0656f0a01209' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6a4cd57f-e69e-430c-8344-4bc4495fae1e' class='xr-var-data-in' type='checkbox'><label for='data-6a4cd57f-e69e-430c-8344-4bc4495fae1e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-8cdf3797-c3cf-4458-ae3f-5b6304cb460b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8cdf3797-c3cf-4458-ae3f-5b6304cb460b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0bb84c62-88f5-4b51-ad41-1e695ff9a94c' class='xr-var-data-in' type='checkbox'><label for='data-0bb84c62-88f5-4b51-ad41-1e695ff9a94c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14902,7 +14902,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -14931,7 +14931,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-e1410a2d-f4fa-4365-9743-8108e0f798e2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e1410a2d-f4fa-4365-9743-8108e0f798e2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d8b607cf-efa6-4623-9820-ce8c36db21c3' class='xr-var-data-in' type='checkbox'><label for='data-d8b607cf-efa6-4623-9820-ce8c36db21c3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-ddd27a66-306f-4a56-846c-86117ae755a3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ddd27a66-306f-4a56-846c-86117ae755a3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-69aaf507-bb5a-4007-9d62-4cff5d952130' class='xr-var-data-in' type='checkbox'><label for='data-69aaf507-bb5a-4007-9d62-4cff5d952130' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14957,7 +14957,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -14986,7 +14986,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-89d57bb5-6d97-44dd-bc9a-f4893412cc61' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-89d57bb5-6d97-44dd-bc9a-f4893412cc61' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-089d5194-0a5a-4718-b5fa-ad378c62eaa8' class='xr-var-data-in' type='checkbox'><label for='data-089d5194-0a5a-4718-b5fa-ad378c62eaa8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-08fc9c8c-77b2-4b62-899b-e6a54f12524a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-08fc9c8c-77b2-4b62-899b-e6a54f12524a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-af2a1b86-4ae6-4d8d-92cd-1d7ae1d6dd1f' class='xr-var-data-in' type='checkbox'><label for='data-af2a1b86-4ae6-4d8d-92cd-1d7ae1d6dd1f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15012,7 +15012,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -15041,7 +15041,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-9f93c84d-49c7-49e0-ba64-9be32c85559b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9f93c84d-49c7-49e0-ba64-9be32c85559b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b0aa63b6-6369-47d2-b7eb-8d2f61d5c081' class='xr-var-data-in' type='checkbox'><label for='data-b0aa63b6-6369-47d2-b7eb-8d2f61d5c081' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-bb4d90bc-d5db-4268-8e82-c079d1b8d345' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bb4d90bc-d5db-4268-8e82-c079d1b8d345' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-75b4bbbd-22b6-4c9f-bd2d-d23067c0c798' class='xr-var-data-in' type='checkbox'><label for='data-75b4bbbd-22b6-4c9f-bd2d-d23067c0c798' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15067,7 +15067,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 9 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -15096,7 +15096,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-91f2845a-f6fc-4691-843b-dc6672ec02f2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-91f2845a-f6fc-4691-843b-dc6672ec02f2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-00327974-50ae-404b-99c5-3841449dfdaa' class='xr-var-data-in' type='checkbox'><label for='data-00327974-50ae-404b-99c5-3841449dfdaa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-8ee09ad8-811d-4db2-950e-3b97d1b13673' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8ee09ad8-811d-4db2-950e-3b97d1b13673' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3ef7f3b9-5685-4bdb-a412-39d4ae77e743' class='xr-var-data-in' type='checkbox'><label for='data-3ef7f3b9-5685-4bdb-a412-39d4ae77e743' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15176,7 +15176,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-642a8372-fbd9-4ef2-b6e6-fa81dcd38b40' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-642a8372-fbd9-4ef2-b6e6-fa81dcd38b40' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6b4ab02c-822c-47de-a3e1-ff97575ae35a' class='xr-var-data-in' type='checkbox'><label for='data-6b4ab02c-822c-47de-a3e1-ff97575ae35a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-ce8d9a88-77d0-4b41-959e-17eca76a00bf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ce8d9a88-77d0-4b41-959e-17eca76a00bf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-378e4a9c-2bf0-4bd3-8d93-e1b43f4df45d' class='xr-var-data-in' type='checkbox'><label for='data-378e4a9c-2bf0-4bd3-8d93-e1b43f4df45d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15232,7 +15232,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-df39d4a9-9585-4868-8bc6-d7f40988d8db' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-df39d4a9-9585-4868-8bc6-d7f40988d8db' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-86b688f9-9969-4c7f-97c0-96d1c1b786b0' class='xr-var-data-in' type='checkbox'><label for='data-86b688f9-9969-4c7f-97c0-96d1c1b786b0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-1b8d9f24-6878-4448-9cee-61be482326e7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1b8d9f24-6878-4448-9cee-61be482326e7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8efbf490-db54-4818-b357-44861728f34b' class='xr-var-data-in' type='checkbox'><label for='data-8efbf490-db54-4818-b357-44861728f34b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15288,7 +15288,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-3a5ea31c-5eae-4aa7-b66d-98228441c31c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3a5ea31c-5eae-4aa7-b66d-98228441c31c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6788694f-cb35-4883-bd23-99d23fe4a6e0' class='xr-var-data-in' type='checkbox'><label for='data-6788694f-cb35-4883-bd23-99d23fe4a6e0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-2ad6a230-70fb-451f-ada8-afe607e5c694' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2ad6a230-70fb-451f-ada8-afe607e5c694' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b503ca9e-9646-487e-8793-97db555d4558' class='xr-var-data-in' type='checkbox'><label for='data-b503ca9e-9646-487e-8793-97db555d4558' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15368,7 +15368,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-fba2b297-716c-4af6-8c07-0553f90002ab' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-fba2b297-716c-4af6-8c07-0553f90002ab' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3e527548-f286-4632-97d7-2dd79edb0e3c' class='xr-var-data-in' type='checkbox'><label for='data-3e527548-f286-4632-97d7-2dd79edb0e3c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-f70febdd-42b8-4ade-8571-aa2d47234d82' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f70febdd-42b8-4ade-8571-aa2d47234d82' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7af69ef0-3de3-47e5-921b-4ad035328f44' class='xr-var-data-in' type='checkbox'><label for='data-7af69ef0-3de3-47e5-921b-4ad035328f44' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15448,7 +15448,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-7fe8d3e1-971d-465e-9415-2e5801d3bce5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7fe8d3e1-971d-465e-9415-2e5801d3bce5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eb60d734-b467-4c89-9983-525a283775f1' class='xr-var-data-in' type='checkbox'><label for='data-eb60d734-b467-4c89-9983-525a283775f1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-8d129bb0-67a3-4e07-8bd7-80f8445cb0fd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8d129bb0-67a3-4e07-8bd7-80f8445cb0fd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-32b461d7-ce38-4b6b-ab6c-fc6970621df3' class='xr-var-data-in' type='checkbox'><label for='data-32b461d7-ce38-4b6b-ab6c-fc6970621df3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15504,7 +15504,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-744ceb27-0ad7-45d5-9cb1-cdbe2342f12f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-744ceb27-0ad7-45d5-9cb1-cdbe2342f12f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-79be1771-e46c-4e48-a9bd-feed53c1e7fd' class='xr-var-data-in' type='checkbox'><label for='data-79be1771-e46c-4e48-a9bd-feed53c1e7fd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-635ba727-6f70-42df-81c8-776b2bb677a6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-635ba727-6f70-42df-81c8-776b2bb677a6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-536a0db2-8ec8-4586-a4a8-54d77191ad5b' class='xr-var-data-in' type='checkbox'><label for='data-536a0db2-8ec8-4586-a4a8-54d77191ad5b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15559,7 +15559,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-2ad4bda6-8ca5-4831-a5cc-d31dfd9f8dba' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2ad4bda6-8ca5-4831-a5cc-d31dfd9f8dba' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-02069041-45fc-419c-aab6-59a0c388c2e8' class='xr-var-data-in' type='checkbox'><label for='data-02069041-45fc-419c-aab6-59a0c388c2e8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-79daadf1-0c7f-4f7b-b716-954b14d07a18' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-79daadf1-0c7f-4f7b-b716-954b14d07a18' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2783db3d-36cf-43db-b08b-d05441a44a44' class='xr-var-data-in' type='checkbox'><label for='data-2783db3d-36cf-43db-b08b-d05441a44a44' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15614,7 +15614,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-b1682a5b-b693-4d79-8bad-2af91b65ee51' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b1682a5b-b693-4d79-8bad-2af91b65ee51' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f3635acb-3877-4bb8-ada0-583701a5434c' class='xr-var-data-in' type='checkbox'><label for='data-f3635acb-3877-4bb8-ada0-583701a5434c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-7f8bd350-b6fa-41ca-b29f-e2ce10c94fe0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7f8bd350-b6fa-41ca-b29f-e2ce10c94fe0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bbddbfd6-0b5e-4a5d-8ade-de97fcb127f0' class='xr-var-data-in' type='checkbox'><label for='data-bbddbfd6-0b5e-4a5d-8ade-de97fcb127f0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15669,7 +15669,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-d06bf038-fae3-44b8-bf92-da4af93267a4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d06bf038-fae3-44b8-bf92-da4af93267a4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b3b04bf4-11de-44c6-b9b9-a02ab0930b03' class='xr-var-data-in' type='checkbox'><label for='data-b3b04bf4-11de-44c6-b9b9-a02ab0930b03' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-bb644f99-73b1-4447-a9a8-0016b0053187' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-bb644f99-73b1-4447-a9a8-0016b0053187' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-29339171-2935-469b-a137-5afdd99bf4ab' class='xr-var-data-in' type='checkbox'><label for='data-29339171-2935-469b-a137-5afdd99bf4ab' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15725,7 +15725,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-e1d5c883-e766-43a7-870b-9d49058caf69' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e1d5c883-e766-43a7-870b-9d49058caf69' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-62323499-bf3d-4d77-b1be-82758e7e8934' class='xr-var-data-in' type='checkbox'><label for='data-62323499-bf3d-4d77-b1be-82758e7e8934' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-28410189-5ac9-4ae8-af0e-a4776a2ac9ca' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-28410189-5ac9-4ae8-af0e-a4776a2ac9ca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0ae6e99e-7a08-40d9-99ce-8264e3193c47' class='xr-var-data-in' type='checkbox'><label for='data-0ae6e99e-7a08-40d9-99ce-8264e3193c47' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15781,7 +15781,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-3da3cc90-31d2-4282-8e4b-d901a06ea0ae' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3da3cc90-31d2-4282-8e4b-d901a06ea0ae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c29edb2b-d1e4-4458-b0b3-2ee7cf66d35d' class='xr-var-data-in' type='checkbox'><label for='data-c29edb2b-d1e4-4458-b0b3-2ee7cf66d35d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-3a41e6f8-b4ac-4080-a32b-25a2f05e237b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3a41e6f8-b4ac-4080-a32b-25a2f05e237b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fec9329c-43be-4df2-8355-39dade745539' class='xr-var-data-in' type='checkbox'><label for='data-fec9329c-43be-4df2-8355-39dade745539' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15837,7 +15837,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-cfce8686-7e54-4f2d-916e-d33d48a31c37' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cfce8686-7e54-4f2d-916e-d33d48a31c37' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5906f6a8-075d-4721-938b-640aba6e8c9c' class='xr-var-data-in' type='checkbox'><label for='data-5906f6a8-075d-4721-938b-640aba6e8c9c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-5fd25755-1294-4d9d-b72d-aa2abb0c9a08' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5fd25755-1294-4d9d-b72d-aa2abb0c9a08' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fcfb6b0c-eafc-4430-8a04-35b67e6fb534' class='xr-var-data-in' type='checkbox'><label for='data-fcfb6b0c-eafc-4430-8a04-35b67e6fb534' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15893,7 +15893,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-75b2ca74-5d34-410e-a3b6-6e54c88c929a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-75b2ca74-5d34-410e-a3b6-6e54c88c929a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d03175a5-745d-466e-9d9d-620429ea9184' class='xr-var-data-in' type='checkbox'><label for='data-d03175a5-745d-466e-9d9d-620429ea9184' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-a8e50a33-e2a9-4312-971b-a2ec7834217a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a8e50a33-e2a9-4312-971b-a2ec7834217a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-168dc81d-c0ca-4d27-89d5-b8a4f200cb6e' class='xr-var-data-in' type='checkbox'><label for='data-168dc81d-c0ca-4d27-89d5-b8a4f200cb6e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15949,7 +15949,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-dc3a1946-e354-43e0-a2eb-f9547e91ecb0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-dc3a1946-e354-43e0-a2eb-f9547e91ecb0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c0a2254-da18-4f5f-9c49-389fcaa2d2f9' class='xr-var-data-in' type='checkbox'><label for='data-5c0a2254-da18-4f5f-9c49-389fcaa2d2f9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-91cacb26-0fe2-4291-9709-b98450a7847a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-91cacb26-0fe2-4291-9709-b98450a7847a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-406528df-d2bf-4060-b2c1-1b5ad25a011b' class='xr-var-data-in' type='checkbox'><label for='data-406528df-d2bf-4060-b2c1-1b5ad25a011b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16005,7 +16005,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-3963392c-aeda-4e39-9a44-6bb10f7afa17' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3963392c-aeda-4e39-9a44-6bb10f7afa17' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c9152611-33c2-4352-9449-e3f37c596a62' class='xr-var-data-in' type='checkbox'><label for='data-c9152611-33c2-4352-9449-e3f37c596a62' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-f42f22c0-b229-4e94-87fe-2a4997bbc488' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f42f22c0-b229-4e94-87fe-2a4997bbc488' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4ac103cd-1225-48bc-9d3a-6ec6d6a4196e' class='xr-var-data-in' type='checkbox'><label for='data-4ac103cd-1225-48bc-9d3a-6ec6d6a4196e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16061,7 +16061,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-2bf91c08-68cd-4767-a954-ccf683a92659' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2bf91c08-68cd-4767-a954-ccf683a92659' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a8561570-c574-4fc1-96f3-7a7cf8628a28' class='xr-var-data-in' type='checkbox'><label for='data-a8561570-c574-4fc1-96f3-7a7cf8628a28' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-790f195b-abc0-4874-a865-798d6ef1a897' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-790f195b-abc0-4874-a865-798d6ef1a897' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8a2ab7da-0662-4b15-a4e6-d98062dd42e9' class='xr-var-data-in' type='checkbox'><label for='data-8a2ab7da-0662-4b15-a4e6-d98062dd42e9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16117,7 +16117,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-ee00a4e2-39e9-4bb3-84dc-5bd21b4d8438' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ee00a4e2-39e9-4bb3-84dc-5bd21b4d8438' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-09918907-9c9c-40d3-83c7-4dea35915e53' class='xr-var-data-in' type='checkbox'><label for='data-09918907-9c9c-40d3-83c7-4dea35915e53' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-ca2e6e26-ffdf-4ecc-a632-b74cf573a4f5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ca2e6e26-ffdf-4ecc-a632-b74cf573a4f5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-69f6c1c0-8893-4aa2-8c07-dffbfdaaa25d' class='xr-var-data-in' type='checkbox'><label for='data-69f6c1c0-8893-4aa2-8c07-dffbfdaaa25d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -16144,7 +16144,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-cf23dce8-c278-4586-a200-55c79a304030' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cf23dce8-c278-4586-a200-55c79a304030' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0ba16666-1bfa-4389-bda1-a0b736b36ea8' class='xr-var-data-in' type='checkbox'><label for='data-0ba16666-1bfa-4389-bda1-a0b736b36ea8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-46d71ce7-9bcf-4f82-94c6-39ff77efb61c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-46d71ce7-9bcf-4f82-94c6-39ff77efb61c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c2baa1b8-174d-41ae-9ae6-952141aea4a0' class='xr-var-data-in' type='checkbox'><label for='data-c2baa1b8-174d-41ae-9ae6-952141aea4a0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -16171,7 +16171,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-a80b8fc3-290c-41ab-96e0-9215ff16fd6f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a80b8fc3-290c-41ab-96e0-9215ff16fd6f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4c6f7576-0ca1-4544-a625-d7f19fa1a6fc' class='xr-var-data-in' type='checkbox'><label for='data-4c6f7576-0ca1-4544-a625-d7f19fa1a6fc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-924fc2c3-d186-48d3-a778-5e458eb94435' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-924fc2c3-d186-48d3-a778-5e458eb94435' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-848e34d6-0fa2-4168-8d90-e4f767578271' class='xr-var-data-in' type='checkbox'><label for='data-848e34d6-0fa2-4168-8d90-e4f767578271' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -16198,7 +16198,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-f550d5df-3858-4842-b93c-44b8e6f99330' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f550d5df-3858-4842-b93c-44b8e6f99330' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3491fae1-0a67-4e6a-8b7b-7fd616fa02f4' class='xr-var-data-in' type='checkbox'><label for='data-3491fae1-0a67-4e6a-8b7b-7fd616fa02f4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-4f2eb3c2-c335-4f5a-910a-d59ed74638b7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4f2eb3c2-c335-4f5a-910a-d59ed74638b7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-993270bc-ff19-41e7-9052-4b5d26696040' class='xr-var-data-in' type='checkbox'><label for='data-993270bc-ff19-41e7-9052-4b5d26696040' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -16225,7 +16225,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-0689e654-6c58-4e6e-9ec7-2ef6e1781acd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0689e654-6c58-4e6e-9ec7-2ef6e1781acd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7436e421-3097-4897-ab62-f1b445ece3d0' class='xr-var-data-in' type='checkbox'><label for='data-7436e421-3097-4897-ab62-f1b445ece3d0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-5551d3d5-6177-44e9-ba92-b4f277cb188a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5551d3d5-6177-44e9-ba92-b4f277cb188a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ea4b9b47-304b-493a-83f8-23354749a9c6' class='xr-var-data-in' type='checkbox'><label for='data-ea4b9b47-304b-493a-83f8-23354749a9c6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -16236,7 +16236,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-08ba8e12-bb2c-4c66-9248-ead5475b84df' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-08ba8e12-bb2c-4c66-9248-ead5475b84df' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f7aa9264-e913-44a7-9f36-969a53b4c249' class='xr-var-data-in' type='checkbox'><label for='data-f7aa9264-e913-44a7-9f36-969a53b4c249' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-96dc7ed2-a788-46ab-88f3-e83df68274a3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-96dc7ed2-a788-46ab-88f3-e83df68274a3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e5f09689-3177-4a84-b915-92d1ad8f439c' class='xr-var-data-in' type='checkbox'><label for='data-e5f09689-3177-4a84-b915-92d1ad8f439c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16291,7 +16291,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-a1fa1467-e8c3-47e5-a3ab-1c1bf82c0448' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a1fa1467-e8c3-47e5-a3ab-1c1bf82c0448' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c3a05e20-6f9e-488c-8847-8a4c3c1bbb6a' class='xr-var-data-in' type='checkbox'><label for='data-c3a05e20-6f9e-488c-8847-8a4c3c1bbb6a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-a34ac513-8605-46eb-a602-e50dd139d728' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a34ac513-8605-46eb-a602-e50dd139d728' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cd97cfff-3ae6-402e-abd8-0ac0ba34e773' class='xr-var-data-in' type='checkbox'><label for='data-cd97cfff-3ae6-402e-abd8-0ac0ba34e773' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16347,7 +16347,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-58ee5531-b6f3-4a1b-a192-8ac0323f6220' class='xr-section-summary-in' type='checkbox'  ><label for='section-58ee5531-b6f3-4a1b-a192-8ac0323f6220' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-c45aae55-937a-4488-b2c9-3ad0d25b6204' class='xr-index-data-in' type='checkbox'/><label for='index-c45aae55-937a-4488-b2c9-3ad0d25b6204' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-8a935597-9f42-4ee5-a149-2a9ac802781f' class='xr-section-summary-in' type='checkbox'  ><label for='section-8a935597-9f42-4ee5-a149-2a9ac802781f' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-e5150ea0-05a3-4cfd-8abc-8d4c6498e321' class='xr-section-summary-in' type='checkbox'  ><label for='section-e5150ea0-05a3-4cfd-8abc-8d4c6498e321' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-496f2821-c5d7-4151-8b66-7f0b59734a9c' class='xr-index-data-in' type='checkbox'/><label for='index-496f2821-c5d7-4151-8b66-7f0b59734a9c' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e872fcd0-656c-4d03-85ff-21e1b2375854' class='xr-section-summary-in' type='checkbox'  ><label for='section-e872fcd0-656c-4d03-85ff-21e1b2375854' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -17004,7 +17004,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
     CaffeineConsumption                  (samples) int64 2kB 4 4 4 3 ... 4 6 5 5
     sample_dp_mean                       (samples) float32 1kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
     call_dosage                          (variants, samples) int64 7MB dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;
-Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-331941d5-a814-4b4c-98a7-1b0a687950a8' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-331941d5-a814-4b4c-98a7-1b0a687950a8' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 250</li><li><span>components</span>: 10</li><li><span>variants</span>: 3491</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-6b46c731-a34c-4ac4-b129-4bd72a637005' class='xr-section-summary-in' type='checkbox'  checked><label for='section-6b46c731-a34c-4ac4-b129-4bd72a637005' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-2b2465a7-f8c3-429a-b481-6dd8f588b19c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2b2465a7-f8c3-429a-b481-6dd8f588b19c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-45165fa4-31ac-4b46-a2bc-66b1621636ac' class='xr-var-data-in' type='checkbox'><label for='data-45165fa4-31ac-4b46-a2bc-66b1621636ac' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-014e8d03-dc25-4192-b512-7dc2dde1dfa4' class='xr-section-summary-in' type='checkbox'  checked><label for='section-014e8d03-dc25-4192-b512-7dc2dde1dfa4' class='xr-section-summary' >Data variables: <span>(48)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_projection</span></div><div class='xr-var-dims'>(samples, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250, 10), meta=np.ndarray&gt;</div><input id='attrs-c72b679b-3b12-4d7c-9d05-74411d4c8d09' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c72b679b-3b12-4d7c-9d05-74411d4c8d09' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-38fb854a-bfba-4543-a3f2-6f5b90c682a1' class='xr-var-data-in' type='checkbox'><label for='data-38fb854a-bfba-4543-a3f2-6f5b90c682a1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (3)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-a7d4807f-ce81-4452-b971-fefaaf408e5b' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a7d4807f-ce81-4452-b971-fefaaf408e5b' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 250</li><li><span>components</span>: 10</li><li><span>variants</span>: 3491</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-69a2e478-4e23-4b7e-a1eb-e416e2c8b68f' class='xr-section-summary-in' type='checkbox'  checked><label for='section-69a2e478-4e23-4b7e-a1eb-e416e2c8b68f' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-b0f2d859-87ad-448d-8f36-bab98b50cf4e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b0f2d859-87ad-448d-8f36-bab98b50cf4e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7f78a699-ed3b-4a16-8779-f44637572591' class='xr-var-data-in' type='checkbox'><label for='data-7f78a699-ed3b-4a16-8779-f44637572591' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-cc4530fb-9eb1-42fe-83dd-551f8ff7f2e5' class='xr-section-summary-in' type='checkbox'  checked><label for='section-cc4530fb-9eb1-42fe-83dd-551f8ff7f2e5' class='xr-section-summary' >Data variables: <span>(48)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_projection</span></div><div class='xr-var-dims'>(samples, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250, 10), meta=np.ndarray&gt;</div><input id='attrs-269faf0d-86ed-4ef6-ac01-cb8a00719b4e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-269faf0d-86ed-4ef6-ac01-cb8a00719b4e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c1942326-bb00-4f82-9316-5e7faaea90dc' class='xr-var-data-in' type='checkbox'><label for='data-c1942326-bb00-4f82-9316-5e7faaea90dc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17059,7 +17059,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_component</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-2d0e1e05-9725-45b0-8de2-a180f2fc5f41' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2d0e1e05-9725-45b0-8de2-a180f2fc5f41' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0604a5b8-4c7d-4326-ba7b-8d9f0347eedc' class='xr-var-data-in' type='checkbox'><label for='data-0604a5b8-4c7d-4326-ba7b-8d9f0347eedc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_component</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-acfa8dbf-e3a4-4cfc-8a02-65533655e5b5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-acfa8dbf-e3a4-4cfc-8a02-65533655e5b5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a8c90f3d-1b7d-4761-b453-da4c0197c261' class='xr-var-data-in' type='checkbox'><label for='data-a8c90f3d-1b7d-4761-b453-da4c0197c261' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17114,7 +17114,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-d8af8bce-3f5b-4c9d-ae16-ceeafbda1500' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d8af8bce-3f5b-4c9d-ae16-ceeafbda1500' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1d97c9a2-d1d7-45c8-9831-075d883e492d' class='xr-var-data-in' type='checkbox'><label for='data-1d97c9a2-d1d7-45c8-9831-075d883e492d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-db57b37f-ed28-42c3-bf55-60512eac4d58' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-db57b37f-ed28-42c3-bf55-60512eac4d58' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2faff88c-ee39-4db7-96c4-333edd2b9581' class='xr-var-data-in' type='checkbox'><label for='data-2faff88c-ee39-4db7-96c4-333edd2b9581' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17169,7 +17169,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance_ratio</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-86a21a42-bba3-4d53-98c9-89811ae8d9f8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-86a21a42-bba3-4d53-98c9-89811ae8d9f8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-90467778-6d2d-44fa-8a53-ef14da7b4d52' class='xr-var-data-in' type='checkbox'><label for='data-90467778-6d2d-44fa-8a53-ef14da7b4d52' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance_ratio</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-0da002ef-bc3b-4a47-b309-507c8e7874e1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0da002ef-bc3b-4a47-b309-507c8e7874e1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7f0db874-9065-4b40-bdb2-57c4e5b49a62' class='xr-var-data-in' type='checkbox'><label for='data-7f0db874-9065-4b40-bdb2-57c4e5b49a62' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17224,7 +17224,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_loading</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-278a7530-a292-4053-aeb6-9ddcccc40ef6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-278a7530-a292-4053-aeb6-9ddcccc40ef6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-181233d3-242a-4baa-a551-7d8f9f5cba46' class='xr-var-data-in' type='checkbox'><label for='data-181233d3-242a-4baa-a551-7d8f9f5cba46' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_loading</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-46c9af23-ba26-48a9-8d7e-1a11f9873be5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-46c9af23-ba26-48a9-8d7e-1a11f9873be5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d851ac57-162b-477c-a8ab-6c45f7c9a131' class='xr-var-data-in' type='checkbox'><label for='data-d851ac57-162b-477c-a8ab-6c45f7c9a131' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17279,7 +17279,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_alternate_allele_count</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int16</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-27f1f85c-7516-4363-afe8-4e150dedbbe4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-27f1f85c-7516-4363-afe8-4e150dedbbe4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ec5ae86d-7cb1-48e0-bf0e-572c3d62912f' class='xr-var-data-in' type='checkbox'><label for='data-ec5ae86d-7cb1-48e0-bf0e-572c3d62912f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_alternate_allele_count</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int16</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-f1f6934b-dda3-4c7c-a4b9-2072416a4f9d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f1f6934b-dda3-4c7c-a4b9-2072416a4f9d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b293c37f-a1ee-464e-a397-da378273da65' class='xr-var-data-in' type='checkbox'><label for='data-b293c37f-a1ee-464e-a397-da378273da65' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17334,7 +17334,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-9ebf7870-7b3c-4695-b647-61ecb6c19a0f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9ebf7870-7b3c-4695-b647-61ecb6c19a0f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ee8d4a36-552e-4e61-8ac0-65ad90fcb149' class='xr-var-data-in' type='checkbox'><label for='data-ee8d4a36-552e-4e61-8ac0-65ad90fcb149' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-d4dcacef-b27f-4fed-9b77-068a0985c7a3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d4dcacef-b27f-4fed-9b77-068a0985c7a3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bffe903d-e9e2-4712-8890-5021fe071886' class='xr-var-data-in' type='checkbox'><label for='data-bffe903d-e9e2-4712-8890-5021fe071886' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17389,7 +17389,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 3), meta=np.ndarray&gt;</div><input id='attrs-9a64bec2-2061-468b-9f76-b4a1675e9b24' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9a64bec2-2061-468b-9f76-b4a1675e9b24' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-56a0a9fa-c0a4-44da-90ba-94afa1467afc' class='xr-var-data-in' type='checkbox'><label for='data-56a0a9fa-c0a4-44da-90ba-94afa1467afc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 3), meta=np.ndarray&gt;</div><input id='attrs-8d009e55-a17b-4e02-8bfb-f7ed862fb4b4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8d009e55-a17b-4e02-8bfb-f7ed862fb4b4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b05c4d1c-61e5-466f-888f-31b13adc3c1b' class='xr-var-data-in' type='checkbox'><label for='data-b05c4d1c-61e5-466f-888f-31b13adc3c1b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
 Counts are sorted following the ordering defined in the VCF specification.
 
 - For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``
@@ -17452,7 +17452,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-a0f7cbfe-db71-455b-94f7-da9659cac05b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a0f7cbfe-db71-455b-94f7-da9659cac05b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-101faf87-288f-4ab2-9c62-c0e83f582822' class='xr-var-data-in' type='checkbox'><label for='data-101faf87-288f-4ab2-9c62-c0e83f582822' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-eb2dd33b-1b48-44ef-af9e-647b51a79e58' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-eb2dd33b-1b48-44ef-af9e-647b51a79e58' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ea2f86d1-01e6-453b-9b00-81ed865975f6' class='xr-var-data-in' type='checkbox'><label for='data-ea2f86d1-01e6-453b-9b00-81ed865975f6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
 ploidy and alleles dimensions. The ordering of genotype strings follows the
 ordering outlined in the VCF specification for arrays of size &quot;G&quot;.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -17509,7 +17509,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-13fdf8ee-6a39-48ac-aae4-f8c29a711ccd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-13fdf8ee-6a39-48ac-aae4-f8c29a711ccd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c0c279d8-e5f7-40cc-bcbf-a2b53141c33b' class='xr-var-data-in' type='checkbox'><label for='data-c0c279d8-e5f7-40cc-bcbf-a2b53141c33b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-470f5e24-98c8-49c2-9809-571f05eac09e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-470f5e24-98c8-49c2-9809-571f05eac09e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f2b4d3fa-49eb-413d-af30-3919f3f041d2' class='xr-var-data-in' type='checkbox'><label for='data-f2b4d3fa-49eb-413d-af30-3919f3f041d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17564,7 +17564,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-200862a9-7d10-4ab4-8040-85ec2af921c5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-200862a9-7d10-4ab4-8040-85ec2af921c5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e14d6d4e-4634-4d40-8cac-ba094558c4f3' class='xr-var-data-in' type='checkbox'><label for='data-e14d6d4e-4634-4d40-8cac-ba094558c4f3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-f27a040a-a099-4808-a135-edc5b45fe92d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f27a040a-a099-4808-a135-edc5b45fe92d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8a85dadd-4d4b-4235-b538-8f259d6d0b97' class='xr-var-data-in' type='checkbox'><label for='data-8a85dadd-4d4b-4235-b538-8f259d6d0b97' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17619,7 +17619,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-fb2f2d5b-69e1-473f-8f70-bcd929b99f8f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb2f2d5b-69e1-473f-8f70-bcd929b99f8f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b842fd06-c0ab-4e15-97b7-2d240b9e8698' class='xr-var-data-in' type='checkbox'><label for='data-b842fd06-c0ab-4e15-97b7-2d240b9e8698' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-3402ab03-0760-4118-a80e-19b8b1c9b4a9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3402ab03-0760-4118-a80e-19b8b1c9b4a9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3faba7e6-4c1d-4dea-aee5-512df795a99d' class='xr-var-data-in' type='checkbox'><label for='data-3faba7e6-4c1d-4dea-aee5-512df795a99d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17674,7 +17674,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-e48beebf-84d7-469f-92db-31d9ab60b741' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e48beebf-84d7-469f-92db-31d9ab60b741' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-51429b11-d67e-4320-996f-b609488a9b7b' class='xr-var-data-in' type='checkbox'><label for='data-51429b11-d67e-4320-996f-b609488a9b7b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-45b1555e-65d1-49b6-837b-f347868b7645' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-45b1555e-65d1-49b6-837b-f347868b7645' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-84c553b7-6538-484f-b454-1415ac428ef9' class='xr-var-data-in' type='checkbox'><label for='data-84c553b7-6538-484f-b454-1415ac428ef9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17729,7 +17729,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-e5cbcb3c-40e1-499e-b1ea-ab5f790b499a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e5cbcb3c-40e1-499e-b1ea-ab5f790b499a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-712cac84-dce9-4254-98df-ed5ff8835bcc' class='xr-var-data-in' type='checkbox'><label for='data-712cac84-dce9-4254-98df-ed5ff8835bcc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-9d7b8d16-2487-4ae3-a026-547985b677aa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9d7b8d16-2487-4ae3-a026-547985b677aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bc32e25d-efca-4c9b-af5e-ec1cf1a544c7' class='xr-var-data-in' type='checkbox'><label for='data-bc32e25d-efca-4c9b-af5e-ec1cf1a544c7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17784,7 +17784,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-13988135-7b94-4c90-9687-dc6705889670' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-13988135-7b94-4c90-9687-dc6705889670' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7d5fdd5b-b5f4-4c2e-bcbf-f3b2cb1c1c3b' class='xr-var-data-in' type='checkbox'><label for='data-7d5fdd5b-b5f4-4c2e-bcbf-f3b2cb1c1c3b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-ff8a4ece-4930-4f02-84d1-b1be296a42fa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ff8a4ece-4930-4f02-84d1-b1be296a42fa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e3818298-0e02-44a3-bd40-9be8b439151b' class='xr-var-data-in' type='checkbox'><label for='data-e3818298-0e02-44a3-bd40-9be8b439151b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17839,7 +17839,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-702f72b4-d837-40dc-b6a9-e228f4b4e547' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-702f72b4-d837-40dc-b6a9-e228f4b4e547' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-89521270-5df9-4d95-a24e-0a87825f638b' class='xr-var-data-in' type='checkbox'><label for='data-89521270-5df9-4d95-a24e-0a87825f638b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-b6e35b38-3dd0-47be-8379-515f6c2b9745' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b6e35b38-3dd0-47be-8379-515f6c2b9745' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4d1fe7a8-9503-4bbe-99c5-e95bc88a4f23' class='xr-var-data-in' type='checkbox'><label for='data-4d1fe7a8-9503-4bbe-99c5-e95bc88a4f23' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -17895,7 +17895,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-f2450031-79da-4f31-aff8-733544f11d8b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f2450031-79da-4f31-aff8-733544f11d8b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9877f05d-117c-4f90-9d02-6b24dc784823' class='xr-var-data-in' type='checkbox'><label for='data-9877f05d-117c-4f90-9d02-6b24dc784823' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-f7100e3f-6f50-4227-9aef-b142fb34295f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f7100e3f-6f50-4227-9aef-b142fb34295f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1d28bf43-35ec-4eb4-bca5-50e8e5c25c21' class='xr-var-data-in' type='checkbox'><label for='data-1d28bf43-35ec-4eb4-bca5-50e8e5c25c21' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17950,7 +17950,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-91a110ef-c236-4693-ab47-c241142eaab7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-91a110ef-c236-4693-ab47-c241142eaab7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1c1bb473-877c-43d5-b702-7790f0be794e' class='xr-var-data-in' type='checkbox'><label for='data-1c1bb473-877c-43d5-b702-7790f0be794e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-597cd1c8-9d77-4c31-bfcb-8150a6b826b9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-597cd1c8-9d77-4c31-bfcb-8150a6b826b9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d76072e9-f694-47e8-8cc7-a269778b60af' class='xr-var-data-in' type='checkbox'><label for='data-d76072e9-f694-47e8-8cc7-a269778b60af' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18005,7 +18005,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-df1e1040-fc43-44c8-8284-6dbdd3acb3e7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-df1e1040-fc43-44c8-8284-6dbdd3acb3e7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c8086d48-15ac-4064-b207-742b693c7454' class='xr-var-data-in' type='checkbox'><label for='data-c8086d48-15ac-4064-b207-742b693c7454' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-07ebf337-68fb-44bb-8cea-d85cc17a4a7a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-07ebf337-68fb-44bb-8cea-d85cc17a4a7a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5427733b-285c-42cf-8dcc-9db46eab70ae' class='xr-var-data-in' type='checkbox'><label for='data-5427733b-285c-42cf-8dcc-9db46eab70ae' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18031,7 +18031,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 7 graph layers </td>
+                        <td colspan="2"> 1 chunks in 9 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -18060,7 +18060,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-43ff5189-6124-41f6-9cee-3ca4ac54363b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-43ff5189-6124-41f6-9cee-3ca4ac54363b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-919f7d6e-5218-456e-a065-e08fb3c1c3a7' class='xr-var-data-in' type='checkbox'><label for='data-919f7d6e-5218-456e-a065-e08fb3c1c3a7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-d8dee09a-0367-4ca3-9157-3ba3d3253a8a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d8dee09a-0367-4ca3-9157-3ba3d3253a8a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d0704418-caaa-43f8-84f6-b21384bfb94e' class='xr-var-data-in' type='checkbox'><label for='data-d0704418-caaa-43f8-84f6-b21384bfb94e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18086,7 +18086,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 8 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -18115,7 +18115,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-f65b48b1-99d9-4a6a-b259-e73c0b1e5aae' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f65b48b1-99d9-4a6a-b259-e73c0b1e5aae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c702b620-3626-47b1-86cd-82b605fa3d41' class='xr-var-data-in' type='checkbox'><label for='data-c702b620-3626-47b1-86cd-82b605fa3d41' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-ccdb1c8b-f73c-4cad-917b-1fa9bf4ad470' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ccdb1c8b-f73c-4cad-917b-1fa9bf4ad470' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0ef6afcf-2cd7-414f-a644-15d0f23917f6' class='xr-var-data-in' type='checkbox'><label for='data-0ef6afcf-2cd7-414f-a644-15d0f23917f6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18141,7 +18141,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -18170,7 +18170,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-ee2027a9-f6f8-465b-bb86-470275290e70' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ee2027a9-f6f8-465b-bb86-470275290e70' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ffced164-0411-4fd4-a101-8349ef00e4d7' class='xr-var-data-in' type='checkbox'><label for='data-ffced164-0411-4fd4-a101-8349ef00e4d7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-25cb7a48-8774-41c7-8314-61986ccca8d6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-25cb7a48-8774-41c7-8314-61986ccca8d6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f483adeb-1047-431d-9d26-3b926255f7e2' class='xr-var-data-in' type='checkbox'><label for='data-f483adeb-1047-431d-9d26-3b926255f7e2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18196,7 +18196,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -18225,7 +18225,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6cfd1e10-8054-442b-a46b-5ff6d77e094a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6cfd1e10-8054-442b-a46b-5ff6d77e094a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e819d645-adbc-43df-bbb5-5fd10972d6ee' class='xr-var-data-in' type='checkbox'><label for='data-e819d645-adbc-43df-bbb5-5fd10972d6ee' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-f9a42a76-5fb8-4b76-9d1f-1a6414c7b31d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f9a42a76-5fb8-4b76-9d1f-1a6414c7b31d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a0ec9cf8-0772-4bf9-a678-1e62da6f1f67' class='xr-var-data-in' type='checkbox'><label for='data-a0ec9cf8-0772-4bf9-a678-1e62da6f1f67' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18251,7 +18251,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 6 graph layers </td>
+                        <td colspan="2"> 1 chunks in 8 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -18280,7 +18280,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-12ffc820-29de-4186-8238-3d3884e4b84f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-12ffc820-29de-4186-8238-3d3884e4b84f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-44d7ee72-50ef-452f-aefe-069adf9b8711' class='xr-var-data-in' type='checkbox'><label for='data-44d7ee72-50ef-452f-aefe-069adf9b8711' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-a5593052-ec59-4d4c-9874-c9eb25295403' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a5593052-ec59-4d4c-9874-c9eb25295403' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bd177384-8220-4774-bb62-89d1868dcf3b' class='xr-var-data-in' type='checkbox'><label for='data-bd177384-8220-4774-bb62-89d1868dcf3b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18306,7 +18306,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
                     </tr>
                     <tr>
                         <th> Dask graph </th>
-                        <td colspan="2"> 1 chunks in 9 graph layers </td>
+                        <td colspan="2"> 1 chunks in 11 graph layers </td>
                     </tr>
                     <tr>
                         <th> Data type </th>
@@ -18335,7 +18335,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-cf6ba986-8b87-43d7-a66f-13452949d3ce' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cf6ba986-8b87-43d7-a66f-13452949d3ce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d4b2db1f-b178-48b5-b33a-fee2d23b7c3c' class='xr-var-data-in' type='checkbox'><label for='data-d4b2db1f-b178-48b5-b33a-fee2d23b7c3c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-5c34de4b-3893-41a2-9231-9adc77488e02' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5c34de4b-3893-41a2-9231-9adc77488e02' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9765e071-6c49-4a1f-96c2-42677b762e48' class='xr-var-data-in' type='checkbox'><label for='data-9765e071-6c49-4a1f-96c2-42677b762e48' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18413,7 +18413,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-dbab53c5-615f-4b5e-aa90-cab85b27283b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-dbab53c5-615f-4b5e-aa90-cab85b27283b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a45b5260-d775-422e-960c-a1db0d80438f' class='xr-var-data-in' type='checkbox'><label for='data-a45b5260-d775-422e-960c-a1db0d80438f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-1b97c8d0-7dd5-4f64-9c2b-413c161ad5bb' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1b97c8d0-7dd5-4f64-9c2b-413c161ad5bb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a75765c8-5bab-4b5b-9af9-af32fbfdf6a5' class='xr-var-data-in' type='checkbox'><label for='data-a75765c8-5bab-4b5b-9af9-af32fbfdf6a5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18468,7 +18468,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-7e757cc8-03a4-4e25-a55a-33d0470a3e7f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7e757cc8-03a4-4e25-a55a-33d0470a3e7f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5a02e483-7a2c-4706-932b-963ab60b9edd' class='xr-var-data-in' type='checkbox'><label for='data-5a02e483-7a2c-4706-932b-963ab60b9edd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-f7a84161-a77a-45dd-aadc-f0acf1828af2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f7a84161-a77a-45dd-aadc-f0acf1828af2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-60c175e8-fe37-481b-80a5-a852d2eefd2c' class='xr-var-data-in' type='checkbox'><label for='data-60c175e8-fe37-481b-80a5-a852d2eefd2c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18523,7 +18523,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-12ff5487-a073-4cbd-bba4-b1e0109488e0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-12ff5487-a073-4cbd-bba4-b1e0109488e0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-83c32b27-37c8-4de0-8cf0-22317609242e' class='xr-var-data-in' type='checkbox'><label for='data-83c32b27-37c8-4de0-8cf0-22317609242e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-69cbd82d-46ee-4f3f-9497-76153cd15a90' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-69cbd82d-46ee-4f3f-9497-76153cd15a90' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2d23809e-c600-463a-9c82-41735fac8d49' class='xr-var-data-in' type='checkbox'><label for='data-2d23809e-c600-463a-9c82-41735fac8d49' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18601,7 +18601,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-1735c8d0-fd24-4946-b9c6-1a5c96207ef6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1735c8d0-fd24-4946-b9c6-1a5c96207ef6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-63df1b21-1447-4300-9dd9-38d7595605e9' class='xr-var-data-in' type='checkbox'><label for='data-63df1b21-1447-4300-9dd9-38d7595605e9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-760223d3-d9d7-4dca-b217-3806b4eb897d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-760223d3-d9d7-4dca-b217-3806b4eb897d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-73be8e1a-9957-4fcc-93c3-54d6f5bd668b' class='xr-var-data-in' type='checkbox'><label for='data-73be8e1a-9957-4fcc-93c3-54d6f5bd668b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18679,7 +18679,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-54689f8a-eb2b-4fc9-9326-b2f560222b7c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-54689f8a-eb2b-4fc9-9326-b2f560222b7c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c65c9e4f-9d68-4122-a617-17e6b15c334f' class='xr-var-data-in' type='checkbox'><label for='data-c65c9e4f-9d68-4122-a617-17e6b15c334f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-9e54e04e-d537-4edc-9d2b-010e11f5c788' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9e54e04e-d537-4edc-9d2b-010e11f5c788' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6ea782cb-da86-41e1-ac8b-a275a09241cc' class='xr-var-data-in' type='checkbox'><label for='data-6ea782cb-da86-41e1-ac8b-a275a09241cc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18734,7 +18734,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-a10b6b47-a279-4c11-abc4-957ac340ef51' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a10b6b47-a279-4c11-abc4-957ac340ef51' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2e6b151e-9697-4cf0-a744-10801011460a' class='xr-var-data-in' type='checkbox'><label for='data-2e6b151e-9697-4cf0-a744-10801011460a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-a3babaa0-a48b-4eb5-8aab-4a16ae0e17c2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a3babaa0-a48b-4eb5-8aab-4a16ae0e17c2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bb5a996b-65d7-4e49-a036-52860a1bda06' class='xr-var-data-in' type='checkbox'><label for='data-bb5a996b-65d7-4e49-a036-52860a1bda06' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18789,7 +18789,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-d37d84fd-e88c-4b12-ab28-f3c9e9600490' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d37d84fd-e88c-4b12-ab28-f3c9e9600490' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-21c50c0a-72a7-4a4d-a8b5-6a8814439a80' class='xr-var-data-in' type='checkbox'><label for='data-21c50c0a-72a7-4a4d-a8b5-6a8814439a80' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-c82168f1-bc0c-483a-b85c-25a52c850d9b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c82168f1-bc0c-483a-b85c-25a52c850d9b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6bb2c88a-5808-4e60-a04a-05a9b7a0c6e5' class='xr-var-data-in' type='checkbox'><label for='data-6bb2c88a-5808-4e60-a04a-05a9b7a0c6e5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18844,7 +18844,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-da2396f9-8a8e-42c9-bfed-bbadea4c7981' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-da2396f9-8a8e-42c9-bfed-bbadea4c7981' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-30853d56-7fd9-4901-bce3-05b474c3e859' class='xr-var-data-in' type='checkbox'><label for='data-30853d56-7fd9-4901-bce3-05b474c3e859' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-4cc88c48-fc52-49d7-bba7-dbf289ba4c25' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4cc88c48-fc52-49d7-bba7-dbf289ba4c25' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7cea3af0-cd2a-4323-a1c0-eb02e6be3e95' class='xr-var-data-in' type='checkbox'><label for='data-7cea3af0-cd2a-4323-a1c0-eb02e6be3e95' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18899,7 +18899,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-df5e47af-9a63-41ff-b751-a05251625453' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-df5e47af-9a63-41ff-b751-a05251625453' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-39a9be09-42d1-4788-b583-2472c6c9921a' class='xr-var-data-in' type='checkbox'><label for='data-39a9be09-42d1-4788-b583-2472c6c9921a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-48db42a6-a32b-486c-8baf-db94664da156' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-48db42a6-a32b-486c-8baf-db94664da156' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1da2481f-18dc-4bd1-863c-14513954112e' class='xr-var-data-in' type='checkbox'><label for='data-1da2481f-18dc-4bd1-863c-14513954112e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of the reference and alternate alleles</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18954,7 +18954,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-56190fd8-ada8-4399-a9bb-7c33f1f136f5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-56190fd8-ada8-4399-a9bb-7c33f1f136f5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dc610657-4ee9-4ed5-b096-d2cc00af3be5' class='xr-var-data-in' type='checkbox'><label for='data-dc610657-4ee9-4ed5-b096-d2cc00af3be5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-38f68654-659d-4337-8758-a8f93e3628d8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-38f68654-659d-4337-8758-a8f93e3628d8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf1a9381-9c7a-476b-9499-8a38e0dab7f5' class='xr-var-data-in' type='checkbox'><label for='data-bf1a9381-9c7a-476b-9499-8a38e0dab7f5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19009,7 +19009,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 1), meta=np.ndarray&gt;</div><input id='attrs-f9ce96ea-5e7d-41e4-aee0-784a580a553d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f9ce96ea-5e7d-41e4-aee0-784a580a553d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d291a609-1fcf-4548-aa54-88a27b545ba5' class='xr-var-data-in' type='checkbox'><label for='data-d291a609-1fcf-4548-aa54-88a27b545ba5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 1), meta=np.ndarray&gt;</div><input id='attrs-f2d12161-98b9-4560-ad54-8b294b0ad39e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f2d12161-98b9-4560-ad54-8b294b0ad39e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e07ba024-e60a-4b25-a99d-80c8e2463da0' class='xr-var-data-in' type='checkbox'><label for='data-e07ba024-e60a-4b25-a99d-80c8e2463da0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Filter status of the variant</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19064,7 +19064,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-a03dab23-158e-46b5-9d7c-253ce0523419' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a03dab23-158e-46b5-9d7c-253ce0523419' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-17962361-2099-4011-8f49-4846e7c52dd2' class='xr-var-data-in' type='checkbox'><label for='data-17962361-2099-4011-8f49-4846e7c52dd2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-ffe9c38f-7068-4c53-bdc6-6d735b012ce1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ffe9c38f-7068-4c53-bdc6-6d735b012ce1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c125eb54-5f7c-4d91-b200-362bd182636e' class='xr-var-data-in' type='checkbox'><label for='data-c125eb54-5f7c-4d91-b200-362bd182636e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>List of unique identifiers where applicable</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19119,7 +19119,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-d465605f-d2c5-4b17-ab51-693cb2dc33db' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d465605f-d2c5-4b17-ab51-693cb2dc33db' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-39d4b1b7-1471-440b-af7f-4dc1ba8b8ff5' class='xr-var-data-in' type='checkbox'><label for='data-39d4b1b7-1471-440b-af7f-4dc1ba8b8ff5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-574ed670-2b31-489e-9501-29969dfd731a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-574ed670-2b31-489e-9501-29969dfd731a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-93660739-b7bc-4fe9-94df-20422f5081ab' class='xr-var-data-in' type='checkbox'><label for='data-93660739-b7bc-4fe9-94df-20422f5081ab' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd></dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19174,7 +19174,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-5a94182b-cf20-4219-b804-c0613d6fa15f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5a94182b-cf20-4219-b804-c0613d6fa15f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-171e24f5-f98d-4186-92bc-0b0105b088fc' class='xr-var-data-in' type='checkbox'><label for='data-171e24f5-f98d-4186-92bc-0b0105b088fc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-1704d848-0e12-4916-95be-6d42adcfa1c5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1704d848-0e12-4916-95be-6d42adcfa1c5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-18b14878-ca0a-44b7-a853-1c2421328137' class='xr-var-data-in' type='checkbox'><label for='data-18b14878-ca0a-44b7-a853-1c2421328137' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>The reference position</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19229,7 +19229,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-a544711c-a852-4af9-a65b-08ff29f9a59a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a544711c-a852-4af9-a65b-08ff29f9a59a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6001a2ef-6cc8-4d11-9083-d98c031b1475' class='xr-var-data-in' type='checkbox'><label for='data-6001a2ef-6cc8-4d11-9083-d98c031b1475' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-57fc804e-4fb9-45d7-8c46-9a56594f6b37' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-57fc804e-4fb9-45d7-8c46-9a56594f6b37' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ef0535ae-f91f-4dcb-97f6-df3b3621da65' class='xr-var-data-in' type='checkbox'><label for='data-ef0535ae-f91f-4dcb-97f6-df3b3621da65' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>description :</span></dt><dd>Phred-scaled quality score</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19284,7 +19284,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-3639e8ed-4112-45f5-a693-4cfcf73efa13' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3639e8ed-4112-45f5-a693-4cfcf73efa13' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-71f54ded-f3b0-4852-958b-54845a8c214b' class='xr-var-data-in' type='checkbox'><label for='data-71f54ded-f3b0-4852-958b-54845a8c214b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-abd6a1e2-8f19-430b-a0a6-9f9acd0e3e57' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-abd6a1e2-8f19-430b-a0a6-9f9acd0e3e57' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f8c426df-65b5-4a44-8f66-e3049cd1ce63' class='xr-var-data-in' type='checkbox'><label for='data-f8c426df-65b5-4a44-8f66-e3049cd1ce63' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19339,7 +19339,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-11d7ca45-8af5-47b0-8f45-3dd5d0cc2d23' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-11d7ca45-8af5-47b0-8f45-3dd5d0cc2d23' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-547ddb91-2321-4ff8-bcbc-44aa6be07e8f' class='xr-var-data-in' type='checkbox'><label for='data-547ddb91-2321-4ff8-bcbc-44aa6be07e8f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-889faab3-9498-4478-8224-213ed1944c16' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-889faab3-9498-4478-8224-213ed1944c16' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9a800fc6-3142-4b87-8f9b-d30b55c869a5' class='xr-var-data-in' type='checkbox'><label for='data-9a800fc6-3142-4b87-8f9b-d30b55c869a5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -19366,7 +19366,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-fe825885-4b35-436d-9271-0dbcef3547ea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fe825885-4b35-436d-9271-0dbcef3547ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4fad917f-1c3e-4b12-8baf-45f43a957991' class='xr-var-data-in' type='checkbox'><label for='data-4fad917f-1c3e-4b12-8baf-45f43a957991' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-ed2cbb96-1817-4696-83f7-ab098f9a79cb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ed2cbb96-1817-4696-83f7-ab098f9a79cb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a4d16af4-51f2-4814-a84a-04ea12909a7a' class='xr-var-data-in' type='checkbox'><label for='data-a4d16af4-51f2-4814-a84a-04ea12909a7a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -19393,7 +19393,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-5660da12-af7b-41d6-99ff-d438fd838287' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5660da12-af7b-41d6-99ff-d438fd838287' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-84e81349-84fc-41c6-a393-c2a6e0e5c44b' class='xr-var-data-in' type='checkbox'><label for='data-84e81349-84fc-41c6-a393-c2a6e0e5c44b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-e900dd99-8aad-4624-82dd-e15b577f25d9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e900dd99-8aad-4624-82dd-e15b577f25d9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8cb9f85f-bee2-4761-82d7-bc8475433b4d' class='xr-var-data-in' type='checkbox'><label for='data-8cb9f85f-bee2-4761-82d7-bc8475433b4d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -19420,7 +19420,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-c5dd0cd8-6739-476f-be5b-d7414345d3d2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c5dd0cd8-6739-476f-be5b-d7414345d3d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2ab88738-3cdf-41a7-8614-92b901ae9df3' class='xr-var-data-in' type='checkbox'><label for='data-2ab88738-3cdf-41a7-8614-92b901ae9df3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-06633ca9-5750-47cb-81a4-598fab7fb851' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-06633ca9-5750-47cb-81a4-598fab7fb851' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ad9b37c2-83f8-4c1f-a778-5beb1d5aa581' class='xr-var-data-in' type='checkbox'><label for='data-ad9b37c2-83f8-4c1f-a778-5beb1d5aa581' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -19447,7 +19447,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-4703ab71-855b-44c6-9454-f0b101dc7504' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4703ab71-855b-44c6-9454-f0b101dc7504' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-da6b00a5-ee95-426d-b7e9-a8d246c53edb' class='xr-var-data-in' type='checkbox'><label for='data-da6b00a5-ee95-426d-b7e9-a8d246c53edb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-f45f8b08-757c-4c5b-9bfa-d373c56804cf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f45f8b08-757c-4c5b-9bfa-d373c56804cf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bebf665f-ebf0-4079-8dcc-889f540475ae' class='xr-var-data-in' type='checkbox'><label for='data-bebf665f-ebf0-4079-8dcc-889f540475ae' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -19458,7 +19458,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-601e145f-160f-487f-b369-b4480ea75f17' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-601e145f-160f-487f-b369-b4480ea75f17' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-06bf71d8-e753-4fec-9ffa-f6394abddfd5' class='xr-var-data-in' type='checkbox'><label for='data-06bf71d8-e753-4fec-9ffa-f6394abddfd5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-d17de840-ab3f-46b6-95a5-0b9db0e8351a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d17de840-ab3f-46b6-95a5-0b9db0e8351a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d6a7f59c-1caf-4e2a-9401-d8922a17fdf2' class='xr-var-data-in' type='checkbox'><label for='data-d6a7f59c-1caf-4e2a-9401-d8922a17fdf2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19513,7 +19513,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-dff77954-0543-4298-84fa-a85e9629086b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dff77954-0543-4298-84fa-a85e9629086b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c5ea4fc6-0c17-4b7f-9591-71449d12085e' class='xr-var-data-in' type='checkbox'><label for='data-c5ea4fc6-0c17-4b7f-9591-71449d12085e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-5d824bab-3eb9-4d19-a7d9-28768bb773ca' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5d824bab-3eb9-4d19-a7d9-28768bb773ca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf648fe5-25e2-4528-954d-5f075164c4d0' class='xr-var-data-in' type='checkbox'><label for='data-bf648fe5-25e2-4528-954d-5f075164c4d0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19568,7 +19568,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-8e02b457-3ac5-4397-b50a-ae4a16a938fa' class='xr-section-summary-in' type='checkbox'  ><label for='section-8e02b457-3ac5-4397-b50a-ae4a16a938fa' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-5e75293a-61d4-4387-807e-e08b1567f79d' class='xr-index-data-in' type='checkbox'/><label for='index-5e75293a-61d4-4387-807e-e08b1567f79d' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a7f6052b-d3ff-4d3c-9109-2d15e55ad14b' class='xr-section-summary-in' type='checkbox'  ><label for='section-a7f6052b-d3ff-4d3c-9109-2d15e55ad14b' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-ff3a76ea-1321-4f0d-9934-aba8a6677ff6' class='xr-section-summary-in' type='checkbox'  ><label for='section-ff3a76ea-1321-4f0d-9934-aba8a6677ff6' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-21f6835c-e441-4c4a-8336-50d48084a89e' class='xr-index-data-in' type='checkbox'/><label for='index-21f6835c-e441-4c4a-8336-50d48084a89e' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-715f7922-8328-49de-b9c4-a9014eb9b289' class='xr-section-summary-in' type='checkbox'  ><label for='section-715f7922-8328-49de-b9c4-a9014eb9b289' class='xr-section-summary' >Attributes: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>source :</span></dt><dd>bio2zarr-0.1.1</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
diff --git a/latest/examples/relatedness_tutorial.html b/latest/examples/relatedness_tutorial.html
index a8a823fc6..8937eb5fa 100644
--- a/latest/examples/relatedness_tutorial.html
+++ b/latest/examples/relatedness_tutorial.html
@@ -1153,17 +1153,17 @@ <h2>Reading pedigree data<a class="headerlink" href="#reading-pedigree-data" tit
        [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)
 Coordinates:
   * samples  (samples) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
-  * parents  (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-0f08fc19-4ccf-4fa2-aed1-8f77662a357f' class='xr-array-in' type='checkbox' checked><label for='section-0f08fc19-4ccf-4fa2-aed1-8f77662a357f' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;4279&#x27; &#x27;6465&#x27; &#x27;6466&#x27; &#x27;1129&#x27; &#x27;5129&#x27; &#x27;6472&#x27;</span></div><div class='xr-array-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
+  * parents  (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-429ef5fe-98ef-4230-b7a8-82cbdd707504' class='xr-array-in' type='checkbox' checked><label for='section-429ef5fe-98ef-4230-b7a8-82cbdd707504' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;4279&#x27; &#x27;6465&#x27; &#x27;6466&#x27; &#x27;1129&#x27; &#x27;5129&#x27; &#x27;6472&#x27;</span></div><div class='xr-array-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        ...,
        [&#x27;4279&#x27;, &#x27;6465&#x27;],
        [&#x27;6466&#x27;, &#x27;1129&#x27;],
-       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></div></li><li class='xr-section-item'><input id='section-24a8bedf-b67c-4625-96eb-9fe6acbaa485' class='xr-section-summary-in' type='checkbox'  checked><label for='section-24a8bedf-b67c-4625-96eb-9fe6acbaa485' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-4fa477b4-4570-4f1a-8d52-1e3f8e1a2dc7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4fa477b4-4570-4f1a-8d52-1e3f8e1a2dc7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dfd9b0d3-b1f6-4e04-ba36-778ff4740632' class='xr-var-data-in' type='checkbox'><label for='data-dfd9b0d3-b1f6-4e04-ba36-778ff4740632' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-586c6eb1-5593-4bb7-a43b-2c26a82740b2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-586c6eb1-5593-4bb7-a43b-2c26a82740b2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ea76c6f3-53b5-44a6-9a5f-d113d9198ab2' class='xr-var-data-in' type='checkbox'><label for='data-ea76c6f3-53b5-44a6-9a5f-d113d9198ab2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-8e67ed06-440c-49be-b371-7671f7057ab8' class='xr-section-summary-in' type='checkbox'  ><label for='section-8e67ed06-440c-49be-b371-7671f7057ab8' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-60f9dade-23f1-468f-bf98-d101890f1291' class='xr-index-data-in' type='checkbox'/><label for='index-60f9dade-23f1-468f-bf98-d101890f1291' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></div></li><li class='xr-section-item'><input id='section-e7d23d61-6bc3-458a-8e51-245d2f4c2712' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e7d23d61-6bc3-458a-8e51-245d2f4c2712' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-f4a8cbf0-a2f6-42c1-b431-14edb8769647' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f4a8cbf0-a2f6-42c1-b431-14edb8769647' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-910ab730-5ed3-4dff-aee3-d01d6cb246d7' class='xr-var-data-in' type='checkbox'><label for='data-910ab730-5ed3-4dff-aee3-d01d6cb246d7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-9f5435bd-77c7-412d-9eea-de8c67f66b47' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9f5435bd-77c7-412d-9eea-de8c67f66b47' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eb34de70-1dda-4da7-a319-1f77a43bce60' class='xr-var-data-in' type='checkbox'><label for='data-eb34de70-1dda-4da7-a319-1f77a43bce60' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-3d160e5e-73e8-4deb-959d-48046328a193' class='xr-section-summary-in' type='checkbox'  ><label for='section-3d160e5e-73e8-4deb-959d-48046328a193' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-8eb669d9-37e5-47a0-a9bc-3c885ab116e8' class='xr-index-data-in' type='checkbox'/><label for='index-8eb669d9-37e5-47a0-a9bc-3c885ab116e8' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-fefb7f5b-d054-4ae7-849e-6110402c34ab' class='xr-index-data-in' type='checkbox'/><label for='index-fefb7f5b-d054-4ae7-849e-6110402c34ab' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-4b83c865-31bb-45e4-bcb7-eacd8d711690' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-4b83c865-31bb-45e4-bcb7-eacd8d711690' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-c1b796f9-1ece-4bd8-9bfa-c91f8e27e2f5' class='xr-index-data-in' type='checkbox'/><label for='index-c1b796f9-1ece-4bd8-9bfa-c91f8e27e2f5' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-48597f7b-0ed5-424c-b0cf-b52f1bcf9bad' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-48597f7b-0ed5-424c-b0cf-b52f1bcf9bad' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 <p>Note that the index column of the pedigree dataframe (containing the sample IDs) has been translated to <em>coordinates</em> for the “samples” dimension of the data array.
 Likewise, the column names have been used as coordinates of the “parents” dimension.</p>
@@ -1557,17 +1557,17 @@ <h2>Reading pedigree data<a class="headerlink" href="#reading-pedigree-data" tit
   * parents    (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;
 Data variables:
     sample_id  (samples) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
-    parent_id  (samples, parents) object 104kB &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-8f0c56b8-cf63-450e-a315-3b478565122b' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-8f0c56b8-cf63-450e-a315-3b478565122b' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-d8a54d9a-14e5-4563-bfdf-a448d3a9347f' class='xr-section-summary-in' type='checkbox'  checked><label for='section-d8a54d9a-14e5-4563-bfdf-a448d3a9347f' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-74c92954-4c01-4b7e-bb28-986d3ab92639' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-74c92954-4c01-4b7e-bb28-986d3ab92639' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-48ae2b11-3133-46b5-b0bd-19ea376dba26' class='xr-var-data-in' type='checkbox'><label for='data-48ae2b11-3133-46b5-b0bd-19ea376dba26' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-fa49bb80-0af5-471f-a866-6be663113b6f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fa49bb80-0af5-471f-a866-6be663113b6f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eeaa3035-fc20-44b1-877a-02782d4dc246' class='xr-var-data-in' type='checkbox'><label for='data-eeaa3035-fc20-44b1-877a-02782d4dc246' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-fd64b5d4-cd0f-4065-b0b0-6d17e04597a2' class='xr-section-summary-in' type='checkbox'  checked><label for='section-fd64b5d4-cd0f-4065-b0b0-6d17e04597a2' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-1582d3c8-e97f-4fc4-840f-a142517b5d96' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1582d3c8-e97f-4fc4-840f-a142517b5d96' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-39cb776d-5c23-46ce-814a-e5be5a73e577' class='xr-var-data-in' type='checkbox'><label for='data-39cb776d-5c23-46ce-814a-e5be5a73e577' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>parent_id</span></div><div class='xr-var-dims'>(samples, parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</div><input id='attrs-1d0611a5-7875-4e28-93c8-e66ae7d4f8a1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1d0611a5-7875-4e28-93c8-e66ae7d4f8a1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1f9d6972-dad3-4ec9-8fb8-58de14fc288c' class='xr-var-data-in' type='checkbox'><label for='data-1f9d6972-dad3-4ec9-8fb8-58de14fc288c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
+    parent_id  (samples, parents) object 104kB &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-bd03d6e1-5527-4435-ba5c-9c51270ef5df' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-bd03d6e1-5527-4435-ba5c-9c51270ef5df' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-576b533d-29e8-467d-8e10-681b27e9ac12' class='xr-section-summary-in' type='checkbox'  checked><label for='section-576b533d-29e8-467d-8e10-681b27e9ac12' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-5eed097c-83c9-41f7-b7a5-6571574a8a7e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5eed097c-83c9-41f7-b7a5-6571574a8a7e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-372993ed-d9df-4169-a27f-5e0909ef9fce' class='xr-var-data-in' type='checkbox'><label for='data-372993ed-d9df-4169-a27f-5e0909ef9fce' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-ecf626f6-efda-468b-b72b-8424485dbdb0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ecf626f6-efda-468b-b72b-8424485dbdb0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1647ef38-339f-475e-a138-aefa551332be' class='xr-var-data-in' type='checkbox'><label for='data-1647ef38-339f-475e-a138-aefa551332be' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-88e291da-26f0-4e07-b7c9-2d6bfa0e8e63' class='xr-section-summary-in' type='checkbox'  checked><label for='section-88e291da-26f0-4e07-b7c9-2d6bfa0e8e63' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-f673bb27-1956-4806-9955-d5a3026164ce' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f673bb27-1956-4806-9955-d5a3026164ce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-381b749c-b532-4459-a6d7-6cb968656f9f' class='xr-var-data-in' type='checkbox'><label for='data-381b749c-b532-4459-a6d7-6cb968656f9f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>parent_id</span></div><div class='xr-var-dims'>(samples, parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</div><input id='attrs-6ba79ebf-15c9-48ea-8904-5d61b230f985' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6ba79ebf-15c9-48ea-8904-5d61b230f985' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-948f3606-0846-417d-88f0-bb55312a79a3' class='xr-var-data-in' type='checkbox'><label for='data-948f3606-0846-417d-88f0-bb55312a79a3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        ...,
        [&#x27;4279&#x27;, &#x27;6465&#x27;],
        [&#x27;6466&#x27;, &#x27;1129&#x27;],
-       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-8d4f4c42-fd7c-4fa8-8294-30e5448463ca' class='xr-section-summary-in' type='checkbox'  ><label for='section-8d4f4c42-fd7c-4fa8-8294-30e5448463ca' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-f0e2a1cb-5fe6-4b54-9af8-305b46c12b49' class='xr-index-data-in' type='checkbox'/><label for='index-f0e2a1cb-5fe6-4b54-9af8-305b46c12b49' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-1bd4e49d-d87d-49ab-a2f3-f037fb7baaff' class='xr-section-summary-in' type='checkbox'  ><label for='section-1bd4e49d-d87d-49ab-a2f3-f037fb7baaff' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-28d5be11-6588-479a-bea4-d298d4b78fe7' class='xr-index-data-in' type='checkbox'/><label for='index-28d5be11-6588-479a-bea4-d298d4b78fe7' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-3dd27c34-360c-476f-a23b-3d9cd054bdff' class='xr-index-data-in' type='checkbox'/><label for='index-3dd27c34-360c-476f-a23b-3d9cd054bdff' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-29ad0303-7c49-47e8-904e-2bec21fdb26d' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-29ad0303-7c49-47e8-904e-2bec21fdb26d' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-7f70af61-42e0-4bac-b4c3-252f0d366d65' class='xr-index-data-in' type='checkbox'/><label for='index-7f70af61-42e0-4bac-b4c3-252f0d366d65' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-08782c24-d2ca-4ae5-b2a4-01f9a93bbf3f' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-08782c24-d2ca-4ae5-b2a4-01f9a93bbf3f' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 </section>
 <section id="working-with-pedigree-data">
@@ -1967,17 +1967,17 @@ <h2>Working with pedigree data<a class="headerlink" href="#working-with-pedigree
   * samples  (samples) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
   * parents  (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;
 Attributes:
-    comment:  Indices of parent samples with negative values indicating unkno...</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'parent'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-51b062cd-9818-40d6-a949-974c0349086e' class='xr-array-in' type='checkbox' checked><label for='section-51b062cd-9818-40d6-a949-974c0349086e' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>-1 -1 -1 -1 -1 -1 -1 -1 -1 ... 6463 3674 4278 6464 6465 1128 5128 6471</span></div><div class='xr-array-data'><pre>array([[  -1,   -1],
+    comment:  Indices of parent samples with negative values indicating unkno...</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'parent'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-942af68c-0c8a-4631-b914-d033ad0d82f3' class='xr-array-in' type='checkbox' checked><label for='section-942af68c-0c8a-4631-b914-d033ad0d82f3' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>-1 -1 -1 -1 -1 -1 -1 -1 -1 ... 6463 3674 4278 6464 6465 1128 5128 6471</span></div><div class='xr-array-data'><pre>array([[  -1,   -1],
        [  -1,   -1],
        [  -1,   -1],
        ...,
        [4278, 6464],
        [6465, 1128],
-       [5128, 6471]])</pre></div></div></li><li class='xr-section-item'><input id='section-3b0e2436-ba48-44c3-85f7-31875957376e' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3b0e2436-ba48-44c3-85f7-31875957376e' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-cbd2cc87-155b-4c0a-83bb-9fc284b2c432' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cbd2cc87-155b-4c0a-83bb-9fc284b2c432' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-25847ce9-d7a3-496d-8650-b22c515fa72d' class='xr-var-data-in' type='checkbox'><label for='data-25847ce9-d7a3-496d-8650-b22c515fa72d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-5a69e688-61aa-426c-82a5-7b0359364179' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5a69e688-61aa-426c-82a5-7b0359364179' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aca28774-473b-4cc1-805c-969ff55acf49' class='xr-var-data-in' type='checkbox'><label for='data-aca28774-473b-4cc1-805c-969ff55acf49' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-8726abdf-f7fc-4072-aadd-3017303b60be' class='xr-section-summary-in' type='checkbox'  ><label for='section-8726abdf-f7fc-4072-aadd-3017303b60be' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-98030ee6-0f70-41f7-a1ff-b4d62f066d3c' class='xr-index-data-in' type='checkbox'/><label for='index-98030ee6-0f70-41f7-a1ff-b4d62f066d3c' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [5128, 6471]])</pre></div></div></li><li class='xr-section-item'><input id='section-9b3726de-ec9d-42e2-b217-80294be3053c' class='xr-section-summary-in' type='checkbox'  checked><label for='section-9b3726de-ec9d-42e2-b217-80294be3053c' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-7545d36e-671a-41db-8518-17bd810d897b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7545d36e-671a-41db-8518-17bd810d897b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3e166abc-8499-4b4a-afdf-f2c0436885e3' class='xr-var-data-in' type='checkbox'><label for='data-3e166abc-8499-4b4a-afdf-f2c0436885e3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-1ecd5799-918a-4b50-a26b-dc1678bef071' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1ecd5799-918a-4b50-a26b-dc1678bef071' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6eedc243-20f5-4a18-b37e-6010ba43fc0c' class='xr-var-data-in' type='checkbox'><label for='data-6eedc243-20f5-4a18-b37e-6010ba43fc0c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-4dfcd231-0578-4a1e-95de-d629f3ac8315' class='xr-section-summary-in' type='checkbox'  ><label for='section-4dfcd231-0578-4a1e-95de-d629f3ac8315' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-4fc915c4-f05a-4074-a776-2d362400f2a3' class='xr-index-data-in' type='checkbox'/><label for='index-4fc915c4-f05a-4074-a776-2d362400f2a3' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-762eb9e8-aae8-4f7d-a4aa-75d2c01e6b9a' class='xr-index-data-in' type='checkbox'/><label for='index-762eb9e8-aae8-4f7d-a4aa-75d2c01e6b9a' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e718f19f-420f-442a-8078-8a0103e3ec01' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e718f19f-420f-442a-8078-8a0103e3ec01' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Indices of parent samples with negative values indicating unknown parents.</dd></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-56341c6f-3006-40bf-8651-1f0c5799f8fb' class='xr-index-data-in' type='checkbox'/><label for='index-56341c6f-3006-40bf-8651-1f0c5799f8fb' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-86bd1740-474d-425e-b282-341fc9ef0057' class='xr-section-summary-in' type='checkbox'  checked><label for='section-86bd1740-474d-425e-b282-341fc9ef0057' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Indices of parent samples with negative values indicating unknown parents.</dd></dl></div></li></ul></div></div></div></div>
 </div>
 <p>The <code class="docutils literal notranslate"><span class="pre">parent_id</span></code> matrix serves as a robust record of the pedigree structure which preserves the structure of a pedigree if the dataset is subset or reordered.
 The <code class="docutils literal notranslate"><span class="pre">parent</span></code> matrix contains integer indices of the parent samples within the dataset allowing for fast numerical calculations.
@@ -2381,7 +2381,7 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
 dask.array&lt;mul, shape=(6473, 6473), dtype=float64, chunksize=(6473, 6473), chunktype=numpy.ndarray&gt;
 Dimensions without coordinates: samples_0, samples_1
 Attributes:
-    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span>samples_0</span>: 6473</li><li><span>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-a9328ac8-fff4-43ad-91d2-0ada22d417ab' class='xr-array-in' type='checkbox' checked><label for='section-a9328ac8-fff4-43ad-91d2-0ada22d417ab' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>dask.array&lt;chunksize=(6473, 6473), meta=np.ndarray&gt;</span></div><div class='xr-array-data'><table>
+    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span>samples_0</span>: 6473</li><li><span>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-0c046fb1-f45a-4c28-9f2a-1b2f71ed1fba' class='xr-array-in' type='checkbox' checked><label for='section-0c046fb1-f45a-4c28-9f2a-1b2f71ed1fba' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>dask.array&lt;chunksize=(6473, 6473), meta=np.ndarray&gt;</span></div><div class='xr-array-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -2436,7 +2436,7 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
 </svg>
         </td>
     </tr>
-</table></div></div></li><li class='xr-section-item'><input id='section-998c150d-f5ba-40b1-abfa-4c319a41c78c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-998c150d-f5ba-40b1-abfa-4c319a41c78c' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-a3997c5f-d184-4dda-a537-1bbad8ac48be' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a3997c5f-d184-4dda-a537-1bbad8ac48be' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-d0991e88-0ada-4bec-9e41-d4689ffc8708' class='xr-section-summary-in' type='checkbox'  checked><label for='section-d0991e88-0ada-4bec-9e41-d4689ffc8708' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
+</table></div></div></li><li class='xr-section-item'><input id='section-9e2b5fa8-3bc5-4ef9-8dae-32b895cc2370' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-9e2b5fa8-3bc5-4ef9-8dae-32b895cc2370' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-1cd42b9a-7077-4d94-aa3c-d07430b915b0' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-1cd42b9a-7077-4d94-aa3c-d07430b915b0' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-9b5756f7-6608-4544-aa8c-fbfe638111ef' class='xr-section-summary-in' type='checkbox'  checked><label for='section-9b5756f7-6608-4544-aa8c-fbfe638111ef' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
 </div>
 <p>Note that the dimensions of the matrices are called <code class="docutils literal notranslate"><span class="pre">samples_0</span></code> and <code class="docutils literal notranslate"><span class="pre">samples_1</span></code> to avoid using a single dimension twice in an xarray DataArray.
 Unfortunately, this means that the coordinates of the <code class="docutils literal notranslate"><span class="pre">samples</span></code> array have not been propagated to the new dimensions.
@@ -2847,7 +2847,7 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
   * samples_0  (samples_0) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
   * samples_1  (samples_1) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
 Attributes:
-    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples_0</span>: 6473</li><li><span class='xr-has-index'>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-0a27d623-7d62-4321-91cf-8149a6306860' class='xr-array-in' type='checkbox' checked><label for='section-0a27d623-7d62-4321-91cf-8149a6306860' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 0.0 0.0 0.0 0.0 ... 0.008972 0.02167 0.01508 0.5325 1.032</span></div><div class='xr-array-data'><pre>array([[1.        , 0.        , 0.        , ..., 0.015625  , 0.        ,
+    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples_0</span>: 6473</li><li><span class='xr-has-index'>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-94761de2-2065-4afa-8d10-086b9ced4405' class='xr-array-in' type='checkbox' checked><label for='section-94761de2-2065-4afa-8d10-086b9ced4405' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 0.0 0.0 0.0 0.0 ... 0.008972 0.02167 0.01508 0.5325 1.032</span></div><div class='xr-array-data'><pre>array([[1.        , 0.        , 0.        , ..., 0.015625  , 0.        ,
         0.        ],
        [0.        , 1.        , 0.        , ..., 0.        , 0.        ,
         0.        ],
@@ -2859,15 +2859,15 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
        [0.        , 0.        , 0.        , ..., 0.01885986, 1.        ,
         0.5324707 ],
        [0.        , 0.        , 0.        , ..., 0.01507568, 0.5324707 ,
-        1.0324707 ]])</pre></div></div></li><li class='xr-section-item'><input id='section-2d974689-7029-498a-a263-5248b5136ce4' class='xr-section-summary-in' type='checkbox'  checked><label for='section-2d974689-7029-498a-a263-5248b5136ce4' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_0</span></div><div class='xr-var-dims'>(samples_0)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-90b27e3e-7c4c-4777-914b-1cc28e334bc1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-90b27e3e-7c4c-4777-914b-1cc28e334bc1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-68c827ff-a653-4a61-abba-19b535e15085' class='xr-var-data-in' type='checkbox'><label for='data-68c827ff-a653-4a61-abba-19b535e15085' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_1</span></div><div class='xr-var-dims'>(samples_1)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-286f1b63-2c05-4985-a4a1-ad6a12e0c1b3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-286f1b63-2c05-4985-a4a1-ad6a12e0c1b3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-69c4a81e-fbc4-416b-b4a8-732b63a31de8' class='xr-var-data-in' type='checkbox'><label for='data-69c4a81e-fbc4-416b-b4a8-732b63a31de8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-9a7d485e-7ea4-4fce-a980-959e8d341a61' class='xr-section-summary-in' type='checkbox'  ><label for='section-9a7d485e-7ea4-4fce-a980-959e8d341a61' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples_0</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-ec3cd162-abc3-42e1-91d6-de1f27131db2' class='xr-index-data-in' type='checkbox'/><label for='index-ec3cd162-abc3-42e1-91d6-de1f27131db2' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+        1.0324707 ]])</pre></div></div></li><li class='xr-section-item'><input id='section-f530368c-b1ee-42bb-99f6-b2b79a90ba13' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f530368c-b1ee-42bb-99f6-b2b79a90ba13' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_0</span></div><div class='xr-var-dims'>(samples_0)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-bb7a77f7-3045-4bda-a734-227bd3ac89ea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bb7a77f7-3045-4bda-a734-227bd3ac89ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6384e92e-ee37-46f6-80a8-8e86d5fbd304' class='xr-var-data-in' type='checkbox'><label for='data-6384e92e-ee37-46f6-80a8-8e86d5fbd304' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_1</span></div><div class='xr-var-dims'>(samples_1)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-76dfdcac-5b4d-4720-a881-314e44661c62' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-76dfdcac-5b4d-4720-a881-314e44661c62' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-41befc77-f34d-4539-be05-e009e8835458' class='xr-var-data-in' type='checkbox'><label for='data-41befc77-f34d-4539-be05-e009e8835458' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f6b4e7e9-03e2-4921-995d-649bab8efa40' class='xr-section-summary-in' type='checkbox'  ><label for='section-f6b4e7e9-03e2-4921-995d-649bab8efa40' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples_0</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-0654f7b6-c093-45fe-aba0-d9f21d92bdfc' class='xr-index-data-in' type='checkbox'/><label for='index-0654f7b6-c093-45fe-aba0-d9f21d92bdfc' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples_0&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples_1</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-803100e4-901d-41af-b1fe-4609590b9666' class='xr-index-data-in' type='checkbox'/><label for='index-803100e4-901d-41af-b1fe-4609590b9666' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+      dtype=&#x27;object&#x27;, name=&#x27;samples_0&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples_1</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-b9ee5b90-db2a-4848-8630-b99ae0d8a0c7' class='xr-index-data-in' type='checkbox'/><label for='index-b9ee5b90-db2a-4848-8630-b99ae0d8a0c7' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples_1&#x27;, length=6473))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-69c67e9f-13d1-4212-b019-5e2144f570ff' class='xr-section-summary-in' type='checkbox'  checked><label for='section-69c67e9f-13d1-4212-b019-5e2144f570ff' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples_1&#x27;, length=6473))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-77b00593-d21b-4a6a-bf89-96eb237c8119' class='xr-section-summary-in' type='checkbox'  checked><label for='section-77b00593-d21b-4a6a-bf89-96eb237c8119' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
 </div>
 <p>We can plot the relationship using matplotlib.</p>
 <div class="cell docutils container">
@@ -3484,20 +3484,20 @@ <h2>Genomic relationships<a class="headerlink" href="#genomic-relationships" tit
        [2., 1., 1., ..., 0., 2., 0.]])
 Coordinates:
   * variants  (variants) object 8kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;997&#x27; &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;
-  * samples   (samples) object 28kB &#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6470&#x27; &#x27;6471&#x27; &#x27;6473&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>variants</span>: 1000</li><li><span class='xr-has-index'>samples</span>: 3534</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-17c563a1-61aa-480f-b389-0fac558cf370' class='xr-array-in' type='checkbox' checked><label for='section-17c563a1-61aa-480f-b389-0fac558cf370' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 2.0 1.0 0.0 1.0 0.0 1.0 ... 1.0 2.0 2.0 1.0 0.0 0.0 2.0 0.0</span></div><div class='xr-array-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
+  * samples   (samples) object 28kB &#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6470&#x27; &#x27;6471&#x27; &#x27;6473&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>variants</span>: 1000</li><li><span class='xr-has-index'>samples</span>: 3534</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-829404f2-db85-4c39-a092-e37236b24965' class='xr-array-in' type='checkbox' checked><label for='section-829404f2-db85-4c39-a092-e37236b24965' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 2.0 1.0 0.0 1.0 0.0 1.0 ... 1.0 2.0 2.0 1.0 0.0 0.0 2.0 0.0</span></div><div class='xr-array-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
        [1., 2., 2., ..., 1., 1., 2.],
        [1., 1., 0., ..., 1., 2., 2.],
        ...,
        [2., 0., 1., ..., 0., 0., 0.],
        [2., 2., 2., ..., 2., 2., 2.],
-       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></div></li><li class='xr-section-item'><input id='section-9cfd1808-f4b0-4bb1-954f-80733a21e596' class='xr-section-summary-in' type='checkbox'  checked><label for='section-9cfd1808-f4b0-4bb1-954f-80733a21e596' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-11794886-83fb-464c-9677-58a0e8c55d87' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-11794886-83fb-464c-9677-58a0e8c55d87' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9cc38811-2bbb-4df3-86f3-c9a548c6f139' class='xr-var-data-in' type='checkbox'><label for='data-9cc38811-2bbb-4df3-86f3-c9a548c6f139' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-c2ebd850-8e60-4422-bc11-2032f496ded7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c2ebd850-8e60-4422-bc11-2032f496ded7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cab11cae-29ac-4238-bd02-65ac170e0ba8' class='xr-var-data-in' type='checkbox'><label for='data-cab11cae-29ac-4238-bd02-65ac170e0ba8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-2918fd29-4cae-4e54-bd2a-647527d291a8' class='xr-section-summary-in' type='checkbox'  ><label for='section-2918fd29-4cae-4e54-bd2a-647527d291a8' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-fd3e1f11-df2f-42f9-b896-fb8dab1664db' class='xr-index-data-in' type='checkbox'/><label for='index-fd3e1f11-df2f-42f9-b896-fb8dab1664db' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></div></li><li class='xr-section-item'><input id='section-47f4265c-8f42-46ec-a944-156e5e2340d1' class='xr-section-summary-in' type='checkbox'  checked><label for='section-47f4265c-8f42-46ec-a944-156e5e2340d1' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-c4d9cfe6-8035-4b30-aa6f-6814b6944b03' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c4d9cfe6-8035-4b30-aa6f-6814b6944b03' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d0ffbeff-5653-49d4-baa4-1498a52b04d9' class='xr-var-data-in' type='checkbox'><label for='data-d0ffbeff-5653-49d4-baa4-1498a52b04d9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-d4a4625b-c3bf-4f56-9498-a39d7597eb91' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d4a4625b-c3bf-4f56-9498-a39d7597eb91' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b47c63cd-a960-4677-9d72-4fc170882959' class='xr-var-data-in' type='checkbox'><label for='data-b47c63cd-a960-4677-9d72-4fc170882959' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-424a2978-461f-4a66-ae8e-b33d50ed4a6d' class='xr-section-summary-in' type='checkbox'  ><label for='section-424a2978-461f-4a66-ae8e-b33d50ed4a6d' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-28ded911-d6a1-4820-b916-24a241325fda' class='xr-index-data-in' type='checkbox'/><label for='index-28ded911-d6a1-4820-b916-24a241325fda' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;991&#x27;, &#x27;992&#x27;, &#x27;993&#x27;, &#x27;994&#x27;, &#x27;995&#x27;, &#x27;996&#x27;, &#x27;997&#x27;, &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-57800a02-c547-44e9-bce5-1bae1d3374eb' class='xr-index-data-in' type='checkbox'/><label for='index-57800a02-c547-44e9-bce5-1bae1d3374eb' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
+      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-baebe945-0a62-4d94-989e-08f9987bcce5' class='xr-index-data-in' type='checkbox'/><label for='index-baebe945-0a62-4d94-989e-08f9987bcce5' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
        ...
        &#x27;6463&#x27;, &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-6275c9a2-a2de-4559-865e-4b4ad3f6b023' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-6275c9a2-a2de-4559-865e-4b4ad3f6b023' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-7cb7e2cc-ef74-4b31-b8e1-9dfb877263c2' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-7cb7e2cc-ef74-4b31-b8e1-9dfb877263c2' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 <p>Next we create a dataset containing the <code class="docutils literal notranslate"><span class="pre">call_dosage</span></code> and <code class="docutils literal notranslate"><span class="pre">sample_id</span></code> variables.</p>
 <div class="cell docutils container">
@@ -3886,20 +3886,20 @@ <h2>Genomic relationships<a class="headerlink" href="#genomic-relationships" tit
   * variants     (variants) object 8kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;
 Data variables:
     sample_id    (samples) object 28kB &#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;
-    call_dosage  (variants, samples) float64 28MB 1.0 0.0 2.0 ... 0.0 2.0 0.0</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-471ccffb-0ec3-4b72-925f-de03f2afead7' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-471ccffb-0ec3-4b72-925f-de03f2afead7' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 3534</li><li><span class='xr-has-index'>variants</span>: 1000</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-b76a77c1-ad94-4e66-8c4b-dec8c2e0efb5' class='xr-section-summary-in' type='checkbox'  checked><label for='section-b76a77c1-ad94-4e66-8c4b-dec8c2e0efb5' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-bc23c176-80c9-471b-8af4-4b1d4e303918' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bc23c176-80c9-471b-8af4-4b1d4e303918' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-19c86005-83fe-4364-b2ee-538104eb0123' class='xr-var-data-in' type='checkbox'><label for='data-19c86005-83fe-4364-b2ee-538104eb0123' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-7f0a9d22-fa7f-4f04-aa37-492cf7434feb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7f0a9d22-fa7f-4f04-aa37-492cf7434feb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a6a9e85b-4b8f-4919-82f2-caf8c41b588b' class='xr-var-data-in' type='checkbox'><label for='data-a6a9e85b-4b8f-4919-82f2-caf8c41b588b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a0f4c4e1-84d0-48d3-9858-d915e741b6ad' class='xr-section-summary-in' type='checkbox'  checked><label for='section-a0f4c4e1-84d0-48d3-9858-d915e741b6ad' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-7ac4474a-bcf9-44d1-aa4a-6c07a6f921fc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7ac4474a-bcf9-44d1-aa4a-6c07a6f921fc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-df315ccb-d93e-4f1e-85de-2aa3d09138f2' class='xr-var-data-in' type='checkbox'><label for='data-df315ccb-d93e-4f1e-85de-2aa3d09138f2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>1.0 0.0 2.0 1.0 ... 0.0 0.0 2.0 0.0</div><input id='attrs-34fcee5a-0fb8-4479-bb7c-e22671bed90e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-34fcee5a-0fb8-4479-bb7c-e22671bed90e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e891530e-7865-4a88-94ac-49ae7970d222' class='xr-var-data-in' type='checkbox'><label for='data-e891530e-7865-4a88-94ac-49ae7970d222' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
+    call_dosage  (variants, samples) float64 28MB 1.0 0.0 2.0 ... 0.0 2.0 0.0</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-1c5a8fcb-e6c6-4370-8a3b-2e7dd24d32be' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-1c5a8fcb-e6c6-4370-8a3b-2e7dd24d32be' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 3534</li><li><span class='xr-has-index'>variants</span>: 1000</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-861e95ed-f535-46f0-8135-25258dcc81a1' class='xr-section-summary-in' type='checkbox'  checked><label for='section-861e95ed-f535-46f0-8135-25258dcc81a1' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-46006a7c-9d20-4537-91aa-d06c4b4c4d89' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-46006a7c-9d20-4537-91aa-d06c4b4c4d89' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-18bec39e-80d3-427a-9ede-5b40e0e232f5' class='xr-var-data-in' type='checkbox'><label for='data-18bec39e-80d3-427a-9ede-5b40e0e232f5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-21c35380-4e48-42eb-9855-7f93232564c0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-21c35380-4e48-42eb-9855-7f93232564c0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-76c5e404-7b4c-4ade-ac3c-589f836780a7' class='xr-var-data-in' type='checkbox'><label for='data-76c5e404-7b4c-4ade-ac3c-589f836780a7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-04024c12-8827-4507-a052-afb2634d91fc' class='xr-section-summary-in' type='checkbox'  checked><label for='section-04024c12-8827-4507-a052-afb2634d91fc' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-f5c33964-a61e-493a-8fe7-06c5c85399b4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f5c33964-a61e-493a-8fe7-06c5c85399b4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-748b5d9d-0c9b-40f8-bfc9-140cd12cd504' class='xr-var-data-in' type='checkbox'><label for='data-748b5d9d-0c9b-40f8-bfc9-140cd12cd504' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>1.0 0.0 2.0 1.0 ... 0.0 0.0 2.0 0.0</div><input id='attrs-16d98d8a-e661-4b5c-9ed9-6018bbfb962e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-16d98d8a-e661-4b5c-9ed9-6018bbfb962e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d2059f6e-0719-46f5-af08-2869755c2b5e' class='xr-var-data-in' type='checkbox'><label for='data-d2059f6e-0719-46f5-af08-2869755c2b5e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
        [1., 2., 2., ..., 1., 1., 2.],
        [1., 1., 0., ..., 1., 2., 2.],
        ...,
        [2., 0., 1., ..., 0., 0., 0.],
        [2., 2., 2., ..., 2., 2., 2.],
-       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-c490e8c4-a1a6-4ec9-8d85-27eed9148c49' class='xr-section-summary-in' type='checkbox'  ><label for='section-c490e8c4-a1a6-4ec9-8d85-27eed9148c49' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-29257601-272e-4e0f-915f-52042efdc8c5' class='xr-index-data-in' type='checkbox'/><label for='index-29257601-272e-4e0f-915f-52042efdc8c5' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
+       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-98bb3d95-371c-43ee-8962-bfa5859c2f0a' class='xr-section-summary-in' type='checkbox'  ><label for='section-98bb3d95-371c-43ee-8962-bfa5859c2f0a' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-2815b72f-2d54-4f8a-907c-56d22bb3b306' class='xr-index-data-in' type='checkbox'/><label for='index-2815b72f-2d54-4f8a-907c-56d22bb3b306' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
        ...
        &#x27;6463&#x27;, &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-0d3a5884-3951-4c8c-ba8a-63a5168e6aed' class='xr-index-data-in' type='checkbox'/><label for='index-0d3a5884-3951-4c8c-ba8a-63a5168e6aed' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-2db320e9-397e-44d5-bd21-f6b4129015d3' class='xr-index-data-in' type='checkbox'/><label for='index-2db320e9-397e-44d5-bd21-f6b4129015d3' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;991&#x27;, &#x27;992&#x27;, &#x27;993&#x27;, &#x27;994&#x27;, &#x27;995&#x27;, &#x27;996&#x27;, &#x27;997&#x27;, &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-2b612766-96e1-413e-97ae-858186bde2ea' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2b612766-96e1-413e-97ae-858186bde2ea' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-840c3dde-a172-4038-bf97-3970c001fc27' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-840c3dde-a172-4038-bf97-3970c001fc27' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 </section>
 <section id="the-vanraden-grm">
@@ -3981,7 +3981,7 @@ <h2>The VanRaden GRM<a class="headerlink" href="#the-vanraden-grm" title="Permal
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2784/892134664.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2856/892134664.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims[&quot;samples&quot;])
 </pre></div>
 </div>
@@ -4085,7 +4085,7 @@ <h2>A better estimate of ancestral allele frequencies<a class="headerlink" href=
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2784/3477141311.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2856/3477141311.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims[&quot;samples&quot;])
 </pre></div>
 </div>
@@ -4157,7 +4157,7 @@ <h2>Weir-Goudet GRM<a class="headerlink" href="#weir-goudet-grm" title="Permalin
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2784/70656024.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2856/70656024.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims[&quot;samples&quot;])
 </pre></div>
 </div>
diff --git a/latest/generated/sgkit.variables.call_dosage_spec.html b/latest/generated/sgkit.variables.call_dosage_spec.html
index 870c7cdfa..aac2968e4 100644
--- a/latest/generated/sgkit.variables.call_dosage_spec.html
+++ b/latest/generated/sgkit.variables.call_dosage_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.call_dosage_spec<a class="headerlink" href="#sgkit-variables-call-dosage-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.call_dosage_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">call_dosage_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='call_dosage',</span> <span class="pre">__doc__='\nDosages,</span> <span class="pre">encoded</span> <span class="pre">as</span> <span class="pre">floats,</span> <span class="pre">with</span> <span class="pre">NaN</span> <span class="pre">indicating</span> <span class="pre">a</span> <span class="pre">missing</span> <span class="pre">value.\nDosages</span> <span class="pre">can</span> <span class="pre">represent</span> <span class="pre">one</span> <span class="pre">of</span> <span class="pre">several</span> <span class="pre">possible</span> <span class="pre">quantities,</span> <span class="pre">e.g.:\n-</span> <span class="pre">Alternate</span> <span class="pre">allele</span> <span class="pre">counts\n-</span> <span class="pre">Recessive</span> <span class="pre">or</span> <span class="pre">dominant</span> <span class="pre">allele</span> <span class="pre">encodings\n-</span> <span class="pre">True</span> <span class="pre">dosages</span> <span class="pre">as</span> <span class="pre">computed</span> <span class="pre">from</span> <span class="pre">imputed</span> <span class="pre">or</span> <span class="pre">probabilistic</span> <span class="pre">variant</span> <span class="pre">calls\n-</span> <span class="pre">Any</span> <span class="pre">other</span> <span class="pre">custom</span> <span class="pre">encoding</span> <span class="pre">in</span> <span class="pre">a</span> <span class="pre">user-defined</span> <span class="pre">variable\n',</span> <span class="pre">kind={'u',</span> <span class="pre">'f',</span> <span class="pre">'i'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'samples'))</span></em><a class="headerlink" href="#sgkit.variables.call_dosage_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">call_dosage_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='call_dosage',</span> <span class="pre">__doc__='\nDosages,</span> <span class="pre">encoded</span> <span class="pre">as</span> <span class="pre">floats,</span> <span class="pre">with</span> <span class="pre">NaN</span> <span class="pre">indicating</span> <span class="pre">a</span> <span class="pre">missing</span> <span class="pre">value.\nDosages</span> <span class="pre">can</span> <span class="pre">represent</span> <span class="pre">one</span> <span class="pre">of</span> <span class="pre">several</span> <span class="pre">possible</span> <span class="pre">quantities,</span> <span class="pre">e.g.:\n-</span> <span class="pre">Alternate</span> <span class="pre">allele</span> <span class="pre">counts\n-</span> <span class="pre">Recessive</span> <span class="pre">or</span> <span class="pre">dominant</span> <span class="pre">allele</span> <span class="pre">encodings\n-</span> <span class="pre">True</span> <span class="pre">dosages</span> <span class="pre">as</span> <span class="pre">computed</span> <span class="pre">from</span> <span class="pre">imputed</span> <span class="pre">or</span> <span class="pre">probabilistic</span> <span class="pre">variant</span> <span class="pre">calls\n-</span> <span class="pre">Any</span> <span class="pre">other</span> <span class="pre">custom</span> <span class="pre">encoding</span> <span class="pre">in</span> <span class="pre">a</span> <span class="pre">user-defined</span> <span class="pre">variable\n',</span> <span class="pre">kind={'u',</span> <span class="pre">'i',</span> <span class="pre">'f'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'samples'))</span></em><a class="headerlink" href="#sgkit.variables.call_dosage_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Dosages, encoded as floats, with NaN indicating a missing value.
 Dosages can represent one of several possible quantities, e.g.:
 - Alternate allele counts
diff --git a/latest/generated/sgkit.variables.interval_contig_name_spec.html b/latest/generated/sgkit.variables.interval_contig_name_spec.html
index e7274f65b..16925cd22 100644
--- a/latest/generated/sgkit.variables.interval_contig_name_spec.html
+++ b/latest/generated/sgkit.variables.interval_contig_name_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.interval_contig_name_spec<a class="headerlink" href="#sgkit-variables-interval-contig-name-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.interval_contig_name_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">interval_contig_name_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='interval_contig_name',</span> <span class="pre">__doc__='Interval</span> <span class="pre">contig</span> <span class="pre">name.</span> <span class="pre">Must</span> <span class="pre">match</span> <span class="pre">a</span> <span class="pre">contig</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">``contigs``</span> <span class="pre">attribute.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=None)</span></em><a class="headerlink" href="#sgkit.variables.interval_contig_name_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">interval_contig_name_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='interval_contig_name',</span> <span class="pre">__doc__='Interval</span> <span class="pre">contig</span> <span class="pre">name.</span> <span class="pre">Must</span> <span class="pre">match</span> <span class="pre">a</span> <span class="pre">contig</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">``contigs``</span> <span class="pre">attribute.',</span> <span class="pre">kind={'S',</span> <span class="pre">'O',</span> <span class="pre">'U'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=None)</span></em><a class="headerlink" href="#sgkit.variables.interval_contig_name_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Interval contig name. Must match a contig defined in the <code class="docutils literal notranslate"><span class="pre">contigs</span></code> attribute.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.parent_id_spec.html b/latest/generated/sgkit.variables.parent_id_spec.html
index cf255f734..ca4aa874e 100644
--- a/latest/generated/sgkit.variables.parent_id_spec.html
+++ b/latest/generated/sgkit.variables.parent_id_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.parent_id_spec<a class="headerlink" href="#sgkit-variables-parent-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.parent_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">parent_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='parent_id',</span> <span class="pre">__doc__='\nUnique</span> <span class="pre">identifiers</span> <span class="pre">of</span> <span class="pre">parent</span> <span class="pre">samples</span> <span class="pre">matching</span> <span class="pre">those</span> <span class="pre">in\n:data:`sgkit.variables.sample_id_spec`.\n',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('samples',</span> <span class="pre">'parents'))</span></em><a class="headerlink" href="#sgkit.variables.parent_id_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">parent_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='parent_id',</span> <span class="pre">__doc__='\nUnique</span> <span class="pre">identifiers</span> <span class="pre">of</span> <span class="pre">parent</span> <span class="pre">samples</span> <span class="pre">matching</span> <span class="pre">those</span> <span class="pre">in\n:data:`sgkit.variables.sample_id_spec`.\n',</span> <span class="pre">kind={'S',</span> <span class="pre">'O',</span> <span class="pre">'U'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('samples',</span> <span class="pre">'parents'))</span></em><a class="headerlink" href="#sgkit.variables.parent_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Unique identifiers of parent samples matching those in
 <a class="reference internal" href="sgkit.variables.sample_id_spec.html#sgkit.variables.sample_id_spec" title="sgkit.variables.sample_id_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.sample_id_spec</span></code></a>.</p>
 </dd></dl>
diff --git a/latest/generated/sgkit.variables.sample_id_spec.html b/latest/generated/sgkit.variables.sample_id_spec.html
index 84f6a555f..dac023ada 100644
--- a/latest/generated/sgkit.variables.sample_id_spec.html
+++ b/latest/generated/sgkit.variables.sample_id_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.sample_id_spec<a class="headerlink" href="#sgkit-variables-sample-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.sample_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">sample_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='sample_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">sample.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('samples',))</span></em><a class="headerlink" href="#sgkit.variables.sample_id_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">sample_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='sample_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">sample.',</span> <span class="pre">kind={'S',</span> <span class="pre">'O',</span> <span class="pre">'U'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('samples',))</span></em><a class="headerlink" href="#sgkit.variables.sample_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>The unique identifier of the sample.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.stat_Fst_spec.html b/latest/generated/sgkit.variables.stat_Fst_spec.html
index bd2faa878..705a48acf 100644
--- a/latest/generated/sgkit.variables.stat_Fst_spec.html
+++ b/latest/generated/sgkit.variables.stat_Fst_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.stat_Fst_spec<a class="headerlink" href="#sgkit-variables-stat-fst-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_Fst_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Fst_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Fst',</span> <span class="pre">__doc__='Fixation</span> <span class="pre">index</span> <span class="pre">(Fst)</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Fst_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Fst_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Fst',</span> <span class="pre">__doc__='Fixation</span> <span class="pre">index</span> <span class="pre">(Fst)</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Fst_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Fixation index (Fst) between pairs of cohorts.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html b/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html
index be8ebe673..88946e58b 100644
--- a/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html
+++ b/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.stat_Tajimas_D_spec<a class="headerlink" href="#sgkit-variables-stat-tajimas-d-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_Tajimas_D_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Tajimas_D_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Tajimas_D',</span> <span class="pre">__doc__='Tajima’s</span> <span class="pre">D</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Tajimas_D_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Tajimas_D_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Tajimas_D',</span> <span class="pre">__doc__='Tajima’s</span> <span class="pre">D</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Tajimas_D_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Tajima’s D for cohorts.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.stat_divergence_spec.html b/latest/generated/sgkit.variables.stat_divergence_spec.html
index bef72d007..1e1261f54 100644
--- a/latest/generated/sgkit.variables.stat_divergence_spec.html
+++ b/latest/generated/sgkit.variables.stat_divergence_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.stat_divergence_spec<a class="headerlink" href="#sgkit-variables-stat-divergence-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_divergence_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_divergence_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_divergence',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">divergence</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_divergence_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_divergence_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_divergence',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">divergence</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_divergence_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Genetic divergence between pairs of cohorts.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.stat_diversity_spec.html b/latest/generated/sgkit.variables.stat_diversity_spec.html
index 763ad54aa..fad470986 100644
--- a/latest/generated/sgkit.variables.stat_diversity_spec.html
+++ b/latest/generated/sgkit.variables.stat_diversity_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.stat_diversity_spec<a class="headerlink" href="#sgkit-variables-stat-diversity-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_diversity_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_diversity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_diversity',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">diversity</span> <span class="pre">(also</span> <span class="pre">known</span> <span class="pre">as</span> <span class="pre">&quot;Tajima’s</span> <span class="pre">pi&quot;)</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_diversity_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_diversity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_diversity',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">diversity</span> <span class="pre">(also</span> <span class="pre">known</span> <span class="pre">as</span> <span class="pre">&quot;Tajima’s</span> <span class="pre">pi&quot;)</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_diversity_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Genetic diversity (also known as “Tajima’s pi”) for cohorts.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html b/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html
index e2818d47b..5d82ce231 100644
--- a/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html
+++ b/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.stat_observed_heterozygosity_spec<a class="headerlink" href="#sgkit-variables-stat-observed-heterozygosity-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_observed_heterozygosity_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_observed_heterozygosity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_observed_heterozygosity',</span> <span class="pre">__doc__='\nObserved</span> <span class="pre">heterozygosity</span> <span class="pre">for</span> <span class="pre">cohorts.\n',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_observed_heterozygosity_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_observed_heterozygosity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_observed_heterozygosity',</span> <span class="pre">__doc__='\nObserved</span> <span class="pre">heterozygosity</span> <span class="pre">for</span> <span class="pre">cohorts.\n',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_observed_heterozygosity_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Observed heterozygosity for cohorts.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.stat_pbs_spec.html b/latest/generated/sgkit.variables.stat_pbs_spec.html
index af0c54014..c7c6c8785 100644
--- a/latest/generated/sgkit.variables.stat_pbs_spec.html
+++ b/latest/generated/sgkit.variables.stat_pbs_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.stat_pbs_spec<a class="headerlink" href="#sgkit-variables-stat-pbs-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_pbs_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_pbs_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_pbs',</span> <span class="pre">__doc__='Population</span> <span class="pre">branching</span> <span class="pre">statistic</span> <span class="pre">for</span> <span class="pre">cohort</span> <span class="pre">triples.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=4,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1',</span> <span class="pre">'cohorts_2'))</span></em><a class="headerlink" href="#sgkit.variables.stat_pbs_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_pbs_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_pbs',</span> <span class="pre">__doc__='Population</span> <span class="pre">branching</span> <span class="pre">statistic</span> <span class="pre">for</span> <span class="pre">cohort</span> <span class="pre">triples.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=4,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1',</span> <span class="pre">'cohorts_2'))</span></em><a class="headerlink" href="#sgkit.variables.stat_pbs_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Population branching statistic for cohort triples.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.variant_id_spec.html b/latest/generated/sgkit.variables.variant_id_spec.html
index 17963f0eb..633769ead 100644
--- a/latest/generated/sgkit.variables.variant_id_spec.html
+++ b/latest/generated/sgkit.variables.variant_id_spec.html
@@ -743,7 +743,7 @@
 <h1>sgkit.variables.variant_id_spec<a class="headerlink" href="#sgkit-variables-variant-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.variant_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">variant.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_id_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">variant.',</span> <span class="pre">kind={'S',</span> <span class="pre">'O',</span> <span class="pre">'U'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>The unique identifier of the variant.</p>
 </dd></dl>
 
diff --git a/latest/searchindex.js b/latest/searchindex.js
index 4460b9a82..16ab876a3 100644
--- a/latest/searchindex.js
+++ b/latest/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["about", "api", "changelog", "contributing", "examples/gwas_tutorial", "examples/index", "examples/relatedness_tutorial", "generated/sgkit.Fst", "generated/sgkit.Garud_H", "generated/sgkit.Tajimas_D", "generated/sgkit.Weir_Goudet_beta", "generated/sgkit.call_allele_frequencies", "generated/sgkit.cohort_allele_frequencies", "generated/sgkit.convert_call_to_index", "generated/sgkit.convert_probability_to_call", "generated/sgkit.count_call_alleles", "generated/sgkit.count_cohort_alleles", "generated/sgkit.count_variant_alleles", "generated/sgkit.count_variant_genotypes", "generated/sgkit.display_genotypes", "generated/sgkit.display_pedigree", "generated/sgkit.divergence", "generated/sgkit.diversity", "generated/sgkit.filter_partial_calls", "generated/sgkit.genee", "generated/sgkit.genomic_relationship", "generated/sgkit.gwas_linear_regression", "generated/sgkit.hardy_weinberg_test", "generated/sgkit.hybrid_inverse_relationship", "generated/sgkit.hybrid_relationship", "generated/sgkit.identity_by_state", "generated/sgkit.individual_heterozygosity", "generated/sgkit.infer_call_ploidy", "generated/sgkit.infer_sample_ploidy", "generated/sgkit.infer_variant_ploidy", "generated/sgkit.invert_relationship_matrix", "generated/sgkit.io.bgen.bgen_to_zarr", "generated/sgkit.io.bgen.read_bgen", "generated/sgkit.io.bgen.rechunk_bgen", "generated/sgkit.io.plink.plink_to_zarr", "generated/sgkit.io.plink.read_plink", "generated/sgkit.io.plink.write_plink", "generated/sgkit.io.plink.zarr_to_plink", "generated/sgkit.io.vcf.concat_zarrs", "generated/sgkit.io.vcf.partition_into_regions", "generated/sgkit.io.vcf.read_vcf", "generated/sgkit.io.vcf.vcf_to_zarr", "generated/sgkit.io.vcf.vcf_to_zarrs", "generated/sgkit.io.vcf.write_vcf", "generated/sgkit.io.vcf.zarr_array_sizes", "generated/sgkit.io.vcf.zarr_to_vcf", "generated/sgkit.ld_matrix", "generated/sgkit.ld_prune", "generated/sgkit.load_dataset", "generated/sgkit.maximal_independent_set", "generated/sgkit.observed_heterozygosity", "generated/sgkit.pairwise_distance", "generated/sgkit.parent_indices", "generated/sgkit.pbs", "generated/sgkit.pc_relate", "generated/sgkit.pedigree_contribution", "generated/sgkit.pedigree_inbreeding", "generated/sgkit.pedigree_inverse_kinship", "generated/sgkit.pedigree_kinship", "generated/sgkit.pedigree_sel", "generated/sgkit.read_scikit_allel_vcfzarr", "generated/sgkit.regenie", "generated/sgkit.sample_stats", "generated/sgkit.save_dataset", "generated/sgkit.simulate_genedrop", "generated/sgkit.simulate_genotype_call_dataset", "generated/sgkit.variables.call_allele_count_spec", "generated/sgkit.variables.call_allele_frequency_spec", "generated/sgkit.variables.call_dosage_mask_spec", "generated/sgkit.variables.call_dosage_spec", "generated/sgkit.variables.call_genotype_complete_mask_spec", "generated/sgkit.variables.call_genotype_complete_spec", "generated/sgkit.variables.call_genotype_fill_spec", "generated/sgkit.variables.call_genotype_index_mask_spec", "generated/sgkit.variables.call_genotype_index_spec", "generated/sgkit.variables.call_genotype_mask_spec", "generated/sgkit.variables.call_genotype_phased_spec", "generated/sgkit.variables.call_genotype_probability_mask_spec", "generated/sgkit.variables.call_genotype_probability_spec", "generated/sgkit.variables.call_genotype_spec", "generated/sgkit.variables.call_heterozygosity_spec", "generated/sgkit.variables.call_ploidy_spec", "generated/sgkit.variables.cohort_allele_count_spec", "generated/sgkit.variables.cohort_allele_frequency_spec", "generated/sgkit.variables.covariates_spec", "generated/sgkit.variables.interval_contig_name_spec", "generated/sgkit.variables.interval_start_spec", "generated/sgkit.variables.interval_stop_spec", "generated/sgkit.variables.ld_prune_index_to_drop_spec", "generated/sgkit.variables.parent_id_spec", "generated/sgkit.variables.parent_spec", "generated/sgkit.variables.pc_relate_phi_spec", "generated/sgkit.variables.regenie_base_prediction_spec", "generated/sgkit.variables.regenie_loco_prediction_spec", "generated/sgkit.variables.regenie_meta_prediction_spec", "generated/sgkit.variables.sample_call_rate_spec", "generated/sgkit.variables.sample_cohort_spec", "generated/sgkit.variables.sample_id_spec", "generated/sgkit.variables.sample_n_called_spec", "generated/sgkit.variables.sample_n_het_spec", "generated/sgkit.variables.sample_n_hom_alt_spec", "generated/sgkit.variables.sample_n_hom_ref_spec", "generated/sgkit.variables.sample_n_non_ref_spec", "generated/sgkit.variables.sample_pca_component_spec", "generated/sgkit.variables.sample_pca_explained_variance_ratio_spec", "generated/sgkit.variables.sample_pca_explained_variance_spec", "generated/sgkit.variables.sample_pca_loading_spec", "generated/sgkit.variables.sample_pca_projection_spec", "generated/sgkit.variables.sample_ploidy_spec", "generated/sgkit.variables.stat_Fst_spec", "generated/sgkit.variables.stat_Garud_h123_spec", "generated/sgkit.variables.stat_Garud_h12_spec", "generated/sgkit.variables.stat_Garud_h1_spec", "generated/sgkit.variables.stat_Garud_h2_h1_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec", "generated/sgkit.variables.stat_Tajimas_D_spec", "generated/sgkit.variables.stat_Weir_Goudet_beta_spec", "generated/sgkit.variables.stat_divergence_spec", "generated/sgkit.variables.stat_diversity_spec", "generated/sgkit.variables.stat_genomic_kinship_spec", "generated/sgkit.variables.stat_genomic_relationship_spec", "generated/sgkit.variables.stat_hybrid_inverse_relationship_spec", "generated/sgkit.variables.stat_hybrid_relationship_spec", "generated/sgkit.variables.stat_identity_by_state_spec", "generated/sgkit.variables.stat_inverse_relationship_spec", "generated/sgkit.variables.stat_observed_heterozygosity_spec", "generated/sgkit.variables.stat_pbs_spec", "generated/sgkit.variables.stat_pedigree_contribution_spec", "generated/sgkit.variables.stat_pedigree_inbreeding_spec", "generated/sgkit.variables.stat_pedigree_inverse_kinship_spec", "generated/sgkit.variables.stat_pedigree_inverse_relationship_spec", "generated/sgkit.variables.stat_pedigree_kinship_spec", "generated/sgkit.variables.stat_pedigree_relationship_spec", "generated/sgkit.variables.traits_spec", "generated/sgkit.variables.variant_allele_count_spec", "generated/sgkit.variables.variant_allele_frequency_spec", "generated/sgkit.variables.variant_allele_spec", "generated/sgkit.variables.variant_allele_total_spec", "generated/sgkit.variables.variant_call_rate_spec", "generated/sgkit.variables.variant_contig_spec", "generated/sgkit.variables.variant_genotype_count_spec", "generated/sgkit.variables.variant_hwe_p_value_spec", "generated/sgkit.variables.variant_id_spec", "generated/sgkit.variables.variant_linreg_beta_spec", "generated/sgkit.variables.variant_linreg_p_value_spec", "generated/sgkit.variables.variant_linreg_t_value_spec", "generated/sgkit.variables.variant_n_called_spec", "generated/sgkit.variables.variant_n_het_spec", "generated/sgkit.variables.variant_n_hom_alt_spec", "generated/sgkit.variables.variant_n_hom_ref_spec", "generated/sgkit.variables.variant_n_non_ref_spec", "generated/sgkit.variables.variant_ploidy_spec", "generated/sgkit.variables.variant_position_spec", "generated/sgkit.variables.variant_score_spec", "generated/sgkit.variables.window_contig_spec", "generated/sgkit.variables.window_start_spec", "generated/sgkit.variables.window_stop_spec", "generated/sgkit.variant_stats", "generated/sgkit.window_by_genome", "generated/sgkit.window_by_interval", "generated/sgkit.window_by_position", "generated/sgkit.window_by_variant", "getting_started", "how_do_i", "index", "news", "news/introducing_sgkit", "user_guide", "vcf"], "filenames": ["about.rst", "api.rst", "changelog.rst", "contributing.rst", "examples/gwas_tutorial.ipynb", "examples/index.rst", "examples/relatedness_tutorial.ipynb", "generated/sgkit.Fst.rst", "generated/sgkit.Garud_H.rst", "generated/sgkit.Tajimas_D.rst", "generated/sgkit.Weir_Goudet_beta.rst", "generated/sgkit.call_allele_frequencies.rst", "generated/sgkit.cohort_allele_frequencies.rst", "generated/sgkit.convert_call_to_index.rst", "generated/sgkit.convert_probability_to_call.rst", "generated/sgkit.count_call_alleles.rst", "generated/sgkit.count_cohort_alleles.rst", "generated/sgkit.count_variant_alleles.rst", "generated/sgkit.count_variant_genotypes.rst", "generated/sgkit.display_genotypes.rst", "generated/sgkit.display_pedigree.rst", "generated/sgkit.divergence.rst", "generated/sgkit.diversity.rst", "generated/sgkit.filter_partial_calls.rst", "generated/sgkit.genee.rst", "generated/sgkit.genomic_relationship.rst", "generated/sgkit.gwas_linear_regression.rst", "generated/sgkit.hardy_weinberg_test.rst", "generated/sgkit.hybrid_inverse_relationship.rst", "generated/sgkit.hybrid_relationship.rst", "generated/sgkit.identity_by_state.rst", "generated/sgkit.individual_heterozygosity.rst", "generated/sgkit.infer_call_ploidy.rst", "generated/sgkit.infer_sample_ploidy.rst", "generated/sgkit.infer_variant_ploidy.rst", "generated/sgkit.invert_relationship_matrix.rst", "generated/sgkit.io.bgen.bgen_to_zarr.rst", "generated/sgkit.io.bgen.read_bgen.rst", "generated/sgkit.io.bgen.rechunk_bgen.rst", "generated/sgkit.io.plink.plink_to_zarr.rst", "generated/sgkit.io.plink.read_plink.rst", "generated/sgkit.io.plink.write_plink.rst", "generated/sgkit.io.plink.zarr_to_plink.rst", "generated/sgkit.io.vcf.concat_zarrs.rst", "generated/sgkit.io.vcf.partition_into_regions.rst", "generated/sgkit.io.vcf.read_vcf.rst", "generated/sgkit.io.vcf.vcf_to_zarr.rst", "generated/sgkit.io.vcf.vcf_to_zarrs.rst", "generated/sgkit.io.vcf.write_vcf.rst", "generated/sgkit.io.vcf.zarr_array_sizes.rst", "generated/sgkit.io.vcf.zarr_to_vcf.rst", "generated/sgkit.ld_matrix.rst", "generated/sgkit.ld_prune.rst", "generated/sgkit.load_dataset.rst", "generated/sgkit.maximal_independent_set.rst", "generated/sgkit.observed_heterozygosity.rst", "generated/sgkit.pairwise_distance.rst", "generated/sgkit.parent_indices.rst", "generated/sgkit.pbs.rst", "generated/sgkit.pc_relate.rst", "generated/sgkit.pedigree_contribution.rst", "generated/sgkit.pedigree_inbreeding.rst", "generated/sgkit.pedigree_inverse_kinship.rst", "generated/sgkit.pedigree_kinship.rst", "generated/sgkit.pedigree_sel.rst", "generated/sgkit.read_scikit_allel_vcfzarr.rst", "generated/sgkit.regenie.rst", "generated/sgkit.sample_stats.rst", "generated/sgkit.save_dataset.rst", "generated/sgkit.simulate_genedrop.rst", "generated/sgkit.simulate_genotype_call_dataset.rst", "generated/sgkit.variables.call_allele_count_spec.rst", "generated/sgkit.variables.call_allele_frequency_spec.rst", "generated/sgkit.variables.call_dosage_mask_spec.rst", "generated/sgkit.variables.call_dosage_spec.rst", "generated/sgkit.variables.call_genotype_complete_mask_spec.rst", "generated/sgkit.variables.call_genotype_complete_spec.rst", "generated/sgkit.variables.call_genotype_fill_spec.rst", "generated/sgkit.variables.call_genotype_index_mask_spec.rst", "generated/sgkit.variables.call_genotype_index_spec.rst", "generated/sgkit.variables.call_genotype_mask_spec.rst", "generated/sgkit.variables.call_genotype_phased_spec.rst", "generated/sgkit.variables.call_genotype_probability_mask_spec.rst", "generated/sgkit.variables.call_genotype_probability_spec.rst", "generated/sgkit.variables.call_genotype_spec.rst", "generated/sgkit.variables.call_heterozygosity_spec.rst", "generated/sgkit.variables.call_ploidy_spec.rst", "generated/sgkit.variables.cohort_allele_count_spec.rst", "generated/sgkit.variables.cohort_allele_frequency_spec.rst", "generated/sgkit.variables.covariates_spec.rst", "generated/sgkit.variables.interval_contig_name_spec.rst", "generated/sgkit.variables.interval_start_spec.rst", "generated/sgkit.variables.interval_stop_spec.rst", "generated/sgkit.variables.ld_prune_index_to_drop_spec.rst", "generated/sgkit.variables.parent_id_spec.rst", "generated/sgkit.variables.parent_spec.rst", "generated/sgkit.variables.pc_relate_phi_spec.rst", "generated/sgkit.variables.regenie_base_prediction_spec.rst", "generated/sgkit.variables.regenie_loco_prediction_spec.rst", "generated/sgkit.variables.regenie_meta_prediction_spec.rst", "generated/sgkit.variables.sample_call_rate_spec.rst", "generated/sgkit.variables.sample_cohort_spec.rst", "generated/sgkit.variables.sample_id_spec.rst", "generated/sgkit.variables.sample_n_called_spec.rst", "generated/sgkit.variables.sample_n_het_spec.rst", "generated/sgkit.variables.sample_n_hom_alt_spec.rst", "generated/sgkit.variables.sample_n_hom_ref_spec.rst", "generated/sgkit.variables.sample_n_non_ref_spec.rst", "generated/sgkit.variables.sample_pca_component_spec.rst", "generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.rst", "generated/sgkit.variables.sample_pca_explained_variance_spec.rst", "generated/sgkit.variables.sample_pca_loading_spec.rst", "generated/sgkit.variables.sample_pca_projection_spec.rst", "generated/sgkit.variables.sample_ploidy_spec.rst", "generated/sgkit.variables.stat_Fst_spec.rst", "generated/sgkit.variables.stat_Garud_h123_spec.rst", "generated/sgkit.variables.stat_Garud_h12_spec.rst", "generated/sgkit.variables.stat_Garud_h1_spec.rst", "generated/sgkit.variables.stat_Garud_h2_h1_spec.rst", "generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.rst", "generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.rst", "generated/sgkit.variables.stat_Tajimas_D_spec.rst", "generated/sgkit.variables.stat_Weir_Goudet_beta_spec.rst", "generated/sgkit.variables.stat_divergence_spec.rst", "generated/sgkit.variables.stat_diversity_spec.rst", "generated/sgkit.variables.stat_genomic_kinship_spec.rst", "generated/sgkit.variables.stat_genomic_relationship_spec.rst", "generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_hybrid_relationship_spec.rst", "generated/sgkit.variables.stat_identity_by_state_spec.rst", "generated/sgkit.variables.stat_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_observed_heterozygosity_spec.rst", "generated/sgkit.variables.stat_pbs_spec.rst", "generated/sgkit.variables.stat_pedigree_contribution_spec.rst", "generated/sgkit.variables.stat_pedigree_inbreeding_spec.rst", "generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.rst", "generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_pedigree_kinship_spec.rst", "generated/sgkit.variables.stat_pedigree_relationship_spec.rst", "generated/sgkit.variables.traits_spec.rst", "generated/sgkit.variables.variant_allele_count_spec.rst", "generated/sgkit.variables.variant_allele_frequency_spec.rst", "generated/sgkit.variables.variant_allele_spec.rst", "generated/sgkit.variables.variant_allele_total_spec.rst", "generated/sgkit.variables.variant_call_rate_spec.rst", "generated/sgkit.variables.variant_contig_spec.rst", "generated/sgkit.variables.variant_genotype_count_spec.rst", "generated/sgkit.variables.variant_hwe_p_value_spec.rst", "generated/sgkit.variables.variant_id_spec.rst", "generated/sgkit.variables.variant_linreg_beta_spec.rst", "generated/sgkit.variables.variant_linreg_p_value_spec.rst", "generated/sgkit.variables.variant_linreg_t_value_spec.rst", "generated/sgkit.variables.variant_n_called_spec.rst", "generated/sgkit.variables.variant_n_het_spec.rst", "generated/sgkit.variables.variant_n_hom_alt_spec.rst", "generated/sgkit.variables.variant_n_hom_ref_spec.rst", "generated/sgkit.variables.variant_n_non_ref_spec.rst", "generated/sgkit.variables.variant_ploidy_spec.rst", "generated/sgkit.variables.variant_position_spec.rst", "generated/sgkit.variables.variant_score_spec.rst", "generated/sgkit.variables.window_contig_spec.rst", "generated/sgkit.variables.window_start_spec.rst", "generated/sgkit.variables.window_stop_spec.rst", "generated/sgkit.variant_stats.rst", "generated/sgkit.window_by_genome.rst", "generated/sgkit.window_by_interval.rst", "generated/sgkit.window_by_position.rst", "generated/sgkit.window_by_variant.rst", "getting_started.rst", "how_do_i.rst", "index.rst", "news.rst", "news/introducing_sgkit.md", "user_guide.rst", "vcf.rst"], "titles": ["About", "API reference", "Changelog", "Contributing to sgkit", "GWAS Tutorial", "Examples", "Relatedness Tutorial", "sgkit.Fst", "sgkit.Garud_H", "sgkit.Tajimas_D", "sgkit.Weir_Goudet_beta", "sgkit.call_allele_frequencies", "sgkit.cohort_allele_frequencies", "sgkit.convert_call_to_index", "sgkit.convert_probability_to_call", "sgkit.count_call_alleles", "sgkit.count_cohort_alleles", "sgkit.count_variant_alleles", "sgkit.count_variant_genotypes", "sgkit.display_genotypes", "sgkit.display_pedigree", "sgkit.divergence", "sgkit.diversity", "sgkit.filter_partial_calls", "sgkit.genee", "sgkit.genomic_relationship", "sgkit.gwas_linear_regression", "sgkit.hardy_weinberg_test", "sgkit.hybrid_inverse_relationship", "sgkit.hybrid_relationship", "sgkit.identity_by_state", "sgkit.individual_heterozygosity", "sgkit.infer_call_ploidy", "sgkit.infer_sample_ploidy", "sgkit.infer_variant_ploidy", "sgkit.invert_relationship_matrix", "sgkit.io.bgen.bgen_to_zarr", "sgkit.io.bgen.read_bgen", "sgkit.io.bgen.rechunk_bgen", "sgkit.io.plink.plink_to_zarr", "sgkit.io.plink.read_plink", "sgkit.io.plink.write_plink", "sgkit.io.plink.zarr_to_plink", "sgkit.io.vcf.concat_zarrs", "sgkit.io.vcf.partition_into_regions", "sgkit.io.vcf.read_vcf", "sgkit.io.vcf.vcf_to_zarr", "sgkit.io.vcf.vcf_to_zarrs", "sgkit.io.vcf.write_vcf", "sgkit.io.vcf.zarr_array_sizes", "sgkit.io.vcf.zarr_to_vcf", "sgkit.ld_matrix", "sgkit.ld_prune", "sgkit.load_dataset", "sgkit.maximal_independent_set", "sgkit.observed_heterozygosity", "sgkit.pairwise_distance", "sgkit.parent_indices", "sgkit.pbs", "sgkit.pc_relate", "sgkit.pedigree_contribution", "sgkit.pedigree_inbreeding", "sgkit.pedigree_inverse_kinship", "sgkit.pedigree_kinship", "sgkit.pedigree_sel", "sgkit.read_scikit_allel_vcfzarr", "sgkit.regenie", "sgkit.sample_stats", "sgkit.save_dataset", "sgkit.simulate_genedrop", "sgkit.simulate_genotype_call_dataset", "sgkit.variables.call_allele_count_spec", "sgkit.variables.call_allele_frequency_spec", "sgkit.variables.call_dosage_mask_spec", "sgkit.variables.call_dosage_spec", "sgkit.variables.call_genotype_complete_mask_spec", "sgkit.variables.call_genotype_complete_spec", "sgkit.variables.call_genotype_fill_spec", "sgkit.variables.call_genotype_index_mask_spec", "sgkit.variables.call_genotype_index_spec", "sgkit.variables.call_genotype_mask_spec", "sgkit.variables.call_genotype_phased_spec", "sgkit.variables.call_genotype_probability_mask_spec", "sgkit.variables.call_genotype_probability_spec", "sgkit.variables.call_genotype_spec", "sgkit.variables.call_heterozygosity_spec", "sgkit.variables.call_ploidy_spec", "sgkit.variables.cohort_allele_count_spec", "sgkit.variables.cohort_allele_frequency_spec", "sgkit.variables.covariates_spec", "sgkit.variables.interval_contig_name_spec", "sgkit.variables.interval_start_spec", "sgkit.variables.interval_stop_spec", "sgkit.variables.ld_prune_index_to_drop_spec", "sgkit.variables.parent_id_spec", "sgkit.variables.parent_spec", "sgkit.variables.pc_relate_phi_spec", "sgkit.variables.regenie_base_prediction_spec", "sgkit.variables.regenie_loco_prediction_spec", "sgkit.variables.regenie_meta_prediction_spec", "sgkit.variables.sample_call_rate_spec", "sgkit.variables.sample_cohort_spec", "sgkit.variables.sample_id_spec", "sgkit.variables.sample_n_called_spec", "sgkit.variables.sample_n_het_spec", "sgkit.variables.sample_n_hom_alt_spec", "sgkit.variables.sample_n_hom_ref_spec", "sgkit.variables.sample_n_non_ref_spec", "sgkit.variables.sample_pca_component_spec", "sgkit.variables.sample_pca_explained_variance_ratio_spec", "sgkit.variables.sample_pca_explained_variance_spec", "sgkit.variables.sample_pca_loading_spec", "sgkit.variables.sample_pca_projection_spec", "sgkit.variables.sample_ploidy_spec", "sgkit.variables.stat_Fst_spec", "sgkit.variables.stat_Garud_h123_spec", "sgkit.variables.stat_Garud_h12_spec", "sgkit.variables.stat_Garud_h1_spec", "sgkit.variables.stat_Garud_h2_h1_spec", "sgkit.variables.stat_Hamilton_Kerr_lambda_spec", "sgkit.variables.stat_Hamilton_Kerr_tau_spec", "sgkit.variables.stat_Tajimas_D_spec", "sgkit.variables.stat_Weir_Goudet_beta_spec", "sgkit.variables.stat_divergence_spec", "sgkit.variables.stat_diversity_spec", "sgkit.variables.stat_genomic_kinship_spec", "sgkit.variables.stat_genomic_relationship_spec", "sgkit.variables.stat_hybrid_inverse_relationship_spec", "sgkit.variables.stat_hybrid_relationship_spec", "sgkit.variables.stat_identity_by_state_spec", "sgkit.variables.stat_inverse_relationship_spec", "sgkit.variables.stat_observed_heterozygosity_spec", "sgkit.variables.stat_pbs_spec", "sgkit.variables.stat_pedigree_contribution_spec", "sgkit.variables.stat_pedigree_inbreeding_spec", "sgkit.variables.stat_pedigree_inverse_kinship_spec", "sgkit.variables.stat_pedigree_inverse_relationship_spec", "sgkit.variables.stat_pedigree_kinship_spec", "sgkit.variables.stat_pedigree_relationship_spec", "sgkit.variables.traits_spec", "sgkit.variables.variant_allele_count_spec", "sgkit.variables.variant_allele_frequency_spec", "sgkit.variables.variant_allele_spec", "sgkit.variables.variant_allele_total_spec", "sgkit.variables.variant_call_rate_spec", "sgkit.variables.variant_contig_spec", "sgkit.variables.variant_genotype_count_spec", "sgkit.variables.variant_hwe_p_value_spec", "sgkit.variables.variant_id_spec", "sgkit.variables.variant_linreg_beta_spec", "sgkit.variables.variant_linreg_p_value_spec", "sgkit.variables.variant_linreg_t_value_spec", "sgkit.variables.variant_n_called_spec", "sgkit.variables.variant_n_het_spec", "sgkit.variables.variant_n_hom_alt_spec", "sgkit.variables.variant_n_hom_ref_spec", "sgkit.variables.variant_n_non_ref_spec", "sgkit.variables.variant_ploidy_spec", "sgkit.variables.variant_position_spec", "sgkit.variables.variant_score_spec", "sgkit.variables.window_contig_spec", "sgkit.variables.window_start_spec", "sgkit.variables.window_stop_spec", "sgkit.variant_stats", "sgkit.window_by_genome", "sgkit.window_by_interval", "sgkit.window_by_position", "sgkit.window_by_variant", "Getting Started", "How do I \u2026", "sgkit: Statistical genetics toolkit in Python", "News", "Introducing sgkit", "User Guide", "Reading VCF"], "terms": {"sgkit": [0, 1, 2, 4, 5, 6, 168, 169, 171], "i": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 74, 76, 79, 81, 84, 86, 91, 92, 93, 95, 101, 103, 104, 105, 106, 107, 108, 109, 110, 112, 113, 133, 143, 145, 146, 152, 153, 154, 155, 156, 157, 158, 160, 161, 162, 163, 165, 166, 168, 170, 171, 172, 173, 174], "fiscal": 0, "sponsor": [0, 172], "project": [0, 3, 6, 26, 112, 172, 173], "numfocu": [0, 172], "nonprofit": 0, "dedic": 0, "support": [0, 2, 3, 6, 7, 9, 13, 18, 21, 22, 25, 27, 37, 40, 48, 58, 60, 66, 67, 163, 171, 172, 173, 174], "open": [0, 4, 6, 39, 40, 43, 44, 45, 46, 47, 53, 68, 173], "sourc": [0, 3, 4, 168, 169, 173], "scientif": [0, 48], "comput": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 51, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 69, 74, 163, 164, 165, 166, 167, 168, 169, 174], "commun": [0, 3], "If": [0, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 50, 51, 52, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 81, 163, 164, 165, 166, 167, 168, 172, 173, 174], "you": [0, 3, 4, 6, 40, 168, 169, 172, 173, 174], "like": [0, 3, 4, 6, 26, 27, 56, 165, 168, 169, 173, 174], "want": [0, 4, 6, 168, 169, 174], "our": [0, 3, 6, 168, 172, 173], "mission": 0, "pleas": [0, 1, 3, 6, 40, 43, 44, 45, 46, 47, 49, 65, 169, 171, 172, 173, 174], "consid": [0, 2, 46, 52, 56, 174], "make": [0, 3, 4, 6, 37, 49, 53, 68, 168, 169, 170, 173, 174], "donat": 0, "effort": 0, "501": 0, "c": [0, 4, 6, 10, 25, 28, 29, 48, 168, 169, 173], "3": [0, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 26, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 55, 56, 57, 58, 61, 62, 63, 65, 66, 69, 71, 72, 75, 76, 77, 80, 82, 83, 84, 87, 88, 98, 114, 123, 166, 167, 168, 169, 173, 174], "non": [0, 2, 3, 4, 6, 10, 11, 12, 15, 16, 17, 24, 25, 32, 33, 34, 45, 46, 47, 61, 62, 63, 69, 71, 72, 77, 84, 88, 140, 173], "profit": 0, "chariti": 0, "unit": [0, 3, 111], "state": [0, 6, 30, 31], "ar": [0, 1, 2, 3, 4, 6, 7, 9, 10, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 54, 55, 56, 58, 59, 60, 61, 62, 63, 65, 66, 67, 69, 70, 73, 75, 76, 80, 81, 82, 107, 108, 110, 120, 133, 146, 156, 163, 165, 166, 167, 168, 169, 173, 174], "tax": 0, "deduct": 0, "allow": [0, 2, 6, 36, 38, 60, 65, 170, 173, 174], "law": 0, "As": [0, 3, 4, 173, 174], "ani": [0, 3, 4, 6, 14, 20, 25, 36, 37, 38, 39, 41, 43, 44, 45, 46, 47, 48, 49, 53, 57, 59, 61, 62, 63, 64, 65, 67, 68, 74, 101, 139, 163, 168, 173, 174], "should": [0, 2, 3, 4, 6, 25, 27, 36, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 70, 120, 168], "consult": 0, "your": [0, 3, 168, 169, 172, 173], "person": [0, 26], "advis": 0, "ir": 0, "particular": [0, 3, 174], "situat": 0, "thi": [1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 17, 18, 19, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 79, 98, 112, 119, 120, 130, 133, 145, 163, 168, 169, 170, 171, 172, 173, 174], "page": [1, 3, 169, 170, 172], "provid": [1, 2, 3, 6, 27, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 51, 52, 59, 65, 66, 70, 98, 168, 170, 172, 173, 174], "an": [1, 2, 3, 4, 6, 13, 25, 26, 28, 29, 31, 35, 37, 39, 40, 45, 46, 47, 48, 54, 56, 59, 60, 61, 62, 63, 69, 119, 133, 159, 168, 169, 171, 172, 173, 174], "auto": [1, 3, 37, 39, 40, 45, 46, 47, 49], "gener": [1, 2, 3, 6, 25, 37, 38, 48, 50, 64, 69, 70, 145, 168, 170, 173, 174], "summari": [1, 4, 70, 168, 170], "": [1, 3, 6, 10, 24, 25, 28, 29, 48, 56, 59, 63, 65, 90, 94, 97, 98, 99, 102, 121, 124, 142, 148, 168, 169, 173, 174], "see": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 43, 44, 45, 46, 47, 53, 54, 55, 57, 58, 59, 65, 66, 67, 68, 69, 119, 120, 163, 164, 165, 166, 167, 168, 170, 173, 174], "data": [1, 2, 3, 10, 25, 26, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 65, 66, 69, 70, 94, 98, 119, 120, 145, 164, 166, 167, 169, 170, 171, 172], "deprec": [1, 3, 43, 44, 45, 46, 47, 49, 63, 65, 174], "sinc": [1, 2, 4, 43, 44, 45, 46, 47, 49, 56, 63, 65, 168, 173, 174], "version": [1, 3, 4, 6, 43, 44, 45, 46, 47, 49, 59, 63, 65, 168, 174], "0": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 43, 44, 45, 46, 47, 49, 51, 52, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 84, 147, 150, 163, 164, 166, 167, 168, 169, 170, 171, 172, 173, 174], "9": [1, 4, 6, 10, 13, 14, 28, 29, 40, 43, 44, 45, 46, 47, 49, 56, 65, 166, 167, 168, 169, 170, 173, 174], "function": [1, 2, 3, 6, 7, 8, 9, 21, 22, 23, 24, 25, 27, 36, 37, 38, 41, 43, 44, 45, 46, 47, 49, 53, 55, 56, 58, 59, 65, 68, 70, 164, 165, 166, 167, 168, 170, 173, 174], "us": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 16, 17, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 119, 145, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 174], "bio2zarr": [1, 2, 4, 43, 44, 45, 46, 47, 49, 65, 174], "packag": [1, 25, 43, 44, 45, 46, 47, 49, 59, 65, 170, 174], "For": [1, 2, 3, 4, 6, 19, 45, 46, 47, 49, 54, 65, 66, 79, 146, 166, 168, 173, 174], "more": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 44, 45, 46, 47, 52, 55, 57, 58, 59, 61, 62, 63, 66, 67, 69, 70, 120, 163, 164, 165, 166, 167, 168, 170, 173, 174], "low": [1, 25, 170], "level": [1, 3, 25, 36, 45, 46, 47, 67, 163, 168, 170], "control": [1, 3, 40, 41, 46, 67, 70, 163, 168, 172, 173, 174], "convert": [1, 2, 4, 6, 13, 14, 36, 37, 39, 41, 42, 46, 47, 48, 50, 170], "from": [1, 2, 3, 6, 10, 11, 14, 15, 16, 17, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 40, 41, 46, 47, 48, 50, 53, 54, 56, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 74, 97, 98, 99, 110, 113, 119, 133, 135, 136, 138, 147, 157, 163, 168, 170, 172, 173, 174], "scikit": [1, 7, 24, 65, 170, 172, 173, 174], "allel": [1, 2, 4, 7, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 21, 22, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 45, 46, 47, 51, 52, 59, 65, 67, 69, 70, 71, 72, 74, 77, 78, 79, 84, 87, 88, 140, 141, 142, 143, 163, 168, 169, 170, 172, 173, 174], "zarr": [1, 2, 4, 36, 38, 39, 42, 43, 45, 46, 47, 48, 49, 50, 53, 65, 68, 168, 170, 171, 172], "represent": [1, 3, 6, 20, 36, 38, 45, 46, 47, 65, 168, 173, 174], "By": [1, 3, 6, 7, 9, 21, 22, 25, 46, 49, 55, 58, 168, 173, 174], "convent": [1, 3, 4, 168, 170], "name": [1, 2, 3, 4, 6, 8, 10, 11, 12, 13, 15, 16, 17, 18, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46, 47, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 89, 90, 139, 145, 163, 165, 166, 167, 168, 169, 174], "singular": [1, 62, 108], "exampl": [1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 21, 22, 23, 25, 28, 29, 30, 31, 35, 45, 46, 47, 48, 52, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66, 69, 139, 164, 166, 167, 168, 170, 173], "genotype_count": [1, 2, 27], "add": [2, 3, 4, 26, 63, 66, 70, 164, 165, 166, 167, 169, 171, 172], "match": [2, 4, 6, 25, 30, 36, 69, 90, 94, 119, 120], "method": [2, 6, 7, 8, 9, 13, 17, 18, 21, 22, 25, 26, 28, 29, 30, 51, 52, 54, 58, 59, 60, 61, 62, 63, 67, 69, 70, 163, 170, 172, 174], "identity_by_st": [2, 10], "timothymillar": 2, "pr": 2, "1229": 2, "gh": [2, 8], "1227": 2, "updat": [2, 3, 4, 6, 172, 173], "gwa": 2, "tutori": [2, 168], "vcf2zarr": [2, 4], "tomwhit": 2, "1258": 2, "1257": 2, "read": [2, 3, 4, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 49, 65, 69, 168, 170, 172], "vcf": [2, 6, 19, 65, 79, 146, 168, 170, 171, 172], "favour": 2, "1233": 2, "1232": 2, "pin": [2, 3], "1230": 2, "numpi": [2, 3, 4, 6, 7, 8, 9, 12, 16, 21, 22, 28, 29, 52, 55, 56, 58, 63, 66, 69, 168, 173], "cbgen": [2, 172], "1228": 2, "1225": 2, "pedigree_contribut": 2, "1093": 2, "963": 2, "pedigree_sel": 2, "1087": 2, "1033": 2, "endelman": [2, 25], "jannink": [2, 25], "estim": [2, 7, 10, 24, 25, 28, 29, 30, 59, 60, 61, 62, 63, 66, 99, 137], "genomic_relationship": [2, 6, 28, 29], "1100": 2, "1062": 2, "display_pedigre": 2, "1104": 2, "1097": 2, "option": [2, 3, 4, 7, 8, 19, 20, 25, 27, 28, 29, 35, 36, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 58, 60, 62, 63, 64, 65, 66, 68, 69, 70, 166, 167, 168, 173, 174], "count": [2, 4, 9, 15, 16, 17, 18, 21, 22, 25, 27, 40, 67, 71, 74, 79, 87, 140, 146, 163, 168, 173], "variant": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 30, 31, 33, 34, 36, 37, 38, 39, 40, 43, 45, 46, 47, 48, 49, 51, 52, 54, 55, 58, 59, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 93, 98, 100, 103, 104, 105, 106, 107, 108, 111, 113, 114, 121, 123, 124, 131, 132, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 161, 162, 163, 165, 166, 167, 168, 170, 172, 173, 174], "directli": [2, 3, 4, 17, 30, 36, 44, 56, 61, 168, 173], "call": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 45, 46, 47, 55, 56, 58, 59, 67, 69, 70, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 86, 100, 103, 104, 105, 106, 107, 113, 144, 152, 153, 154, 155, 156, 157, 163, 164, 165, 166, 167, 168, 169, 173, 174], "genotyp": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 45, 46, 47, 51, 52, 55, 58, 59, 65, 66, 67, 69, 70, 76, 77, 78, 79, 82, 83, 84, 85, 86, 100, 103, 113, 144, 146, 152, 157, 163, 164, 165, 166, 167, 168, 170, 173, 174], "count_variant_allel": [2, 9, 163, 168, 173], "1119": 2, "1116": 2, "simulate_genedrop": 2, "1139": 2, "1107": 2, "perform": [2, 3, 37, 38, 39, 40, 168, 173, 174], "variant_stat": [2, 4, 168, 169, 173], "sample_stat": [2, 4, 169], "error": [2, 6, 35, 45, 46, 66, 168, 169, 173, 174], "miss": [2, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 23, 25, 30, 40, 41, 45, 46, 47, 56, 57, 59, 64, 67, 70, 71, 72, 73, 74, 75, 76, 78, 79, 80, 82, 84, 88, 140, 163, 170, 173], "handl": [2, 3, 168, 174], "valu": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 43, 44, 45, 46, 47, 48, 49, 51, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 69, 70, 71, 72, 73, 74, 75, 77, 79, 80, 82, 84, 88, 95, 101, 110, 111, 120, 125, 130, 133, 137, 140, 147, 149, 150, 161, 162, 164, 165, 166, 167, 168, 170, 173, 174], "most": [2, 3, 6, 51, 52, 59, 168, 173], "field": [2, 24, 38, 39, 40, 41, 45, 46, 47, 48, 51, 65, 70, 174], "were": [2, 3, 4, 6, 119, 145, 170], "mark": 2, "correspond": [2, 3, 4, 6, 11, 12, 15, 16, 17, 25, 27, 28, 29, 39, 40, 45, 46, 47, 48, 59, 64, 65, 71, 72, 78, 79, 88, 89, 139, 140, 145, 168, 169], "fill": [2, 4, 32, 33, 34, 45, 46, 47, 77], "string": [2, 4, 6, 36, 38, 39, 40, 44, 45, 46, 47, 49, 174], "store": [2, 4, 6, 36, 38, 39, 42, 43, 45, 46, 47, 50, 53, 68, 172, 173, 174], "empti": 2, "rather": [2, 3, 4, 6, 24, 28, 29, 173, 174], "than": [2, 3, 4, 6, 14, 19, 24, 28, 29, 32, 36, 37, 44, 45, 46, 47, 48, 59, 61, 62, 63, 65, 69, 173, 174], "similarli": [2, 173], "integ": [2, 4, 6, 13, 36, 37, 39, 40, 44, 45, 46, 47, 57, 63, 64, 65, 69, 79, 145, 168, 169, 173, 174], "int": [2, 8, 19, 25, 27, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 49, 56, 58, 64, 66, 70, 166, 167, 174], "jeromekelleh": 2, "1190": 2, "1192": 2, "max_str_len": 2, "util": [2, 4, 28, 29, 168, 170, 173], "return": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "python": [2, 4, 6, 48, 165, 168, 174], "arrai": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 37, 39, 40, 45, 46, 47, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66, 69, 79, 89, 112, 139, 166, 167, 169, 170, 173, 174], "scalar": [2, 168], "1086": 2, "1085": 2, "turn": 2, "off": [2, 168, 174], "numba": [2, 48], "cach": 2, "default": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "1191": 2, "1156": 2, "xarrai": [2, 3, 4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 28, 29, 35, 45, 46, 47, 53, 55, 58, 66, 68, 70, 164, 166, 167, 168, 169, 170, 172, 173, 174], "repr": [2, 169], "doctest": [2, 3], "1205": 2, "1204": 2, "avoid": [2, 3, 4, 6, 35, 45, 46, 51, 52, 168, 169, 174], "disabl": [2, 14], "jit": [2, 173], "guvectoris": 2, "1199": 2, "1194": 2, "relationship": [2, 25, 28, 29, 35, 59, 61, 62, 63, 69, 126, 127, 128, 130, 136, 138], "matric": [2, 28, 29], "1072": 2, "956": 2, "pairwise_dist": 2, "doc": [2, 3, 37, 39, 40], "benjefferi": 2, "1145": 2, "1142": 2, "format": [2, 3, 4, 6, 19, 40, 45, 46, 47, 65, 168, 171, 172, 173, 174], "matrix": [2, 6, 10, 25, 28, 29, 30, 35, 51, 52, 54, 56, 59, 61, 62, 63, 69, 96, 108, 110, 125, 126, 127, 128, 130, 133, 135, 136, 138, 159], "pairwis": [2, 6, 10, 25, 28, 29, 30, 56, 59, 63, 122, 129, 137], "1148": 2, "1147": 2, "io": [2, 3, 6, 14, 65, 66, 170, 173, 174], "plink": [2, 6, 54, 168, 172], "write_plink": [2, 42, 173], "1003": 2, "926": [2, 168], "phase": [2, 19, 36, 65, 70, 81], "simulate_genotype_call_dataset": [2, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 52, 55, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 173], "1022": 2, "973": 2, "plink_to_zarr": 2, "zarr_to_plink": [2, 173], "conveni": [2, 4, 26, 36, 39, 42, 45, 50, 70, 168, 173], "1047": 2, "1004": 2, "convert_call_to_index": [2, 173], "1050": 2, "1048": 2, "read_chunk_length": [2, 46, 47], "vcf_to_zarr": [2, 43, 45, 48, 65, 173, 174], "These": [2, 3, 6, 25, 27, 66, 110, 111, 168, 173], "reduc": [2, 46, 47, 56, 168], "memori": [2, 4, 36, 37, 38, 39, 40, 45, 46, 47, 48, 54, 61, 168, 169, 173, 174], "usag": [2, 4, 46, 47, 61, 168, 170], "larg": [2, 3, 26, 30, 45, 46, 47, 51, 52, 168, 170, 173, 174], "sampl": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 45, 46, 47, 48, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 89, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 112, 113, 119, 120, 122, 129, 133, 134, 137, 139, 144, 152, 153, 154, 155, 156, 157, 163, 168, 170, 172, 173, 174], "chunk_length": [2, 36, 38, 43, 45, 46, 47, 174], "1044": 2, "1042": 2, "retain_temp_fil": [2, 46], "1046": 2, "1036": 2, "read_vcf": 2, "1052": 2, "hybrid_relationship": [2, 6, 28], "hybrid_inverse_relationship": [2, 29], "invert_relationship_matrix": [2, 6, 28, 29], "1053": 2, "993": [2, 6], "zarr_array_s": 2, "determin": [2, 3, 7, 37, 49, 56, 168], "size": [2, 4, 6, 7, 8, 9, 12, 16, 18, 21, 22, 24, 25, 26, 35, 37, 39, 40, 44, 45, 46, 47, 48, 49, 52, 55, 56, 58, 63, 66, 79, 164, 166, 167, 168, 169, 170, 173], "storag": [2, 4, 6, 39, 43, 44, 45, 46, 47, 49, 53, 68, 168, 170, 173], "1073": 2, "734": 2, "skipna": [2, 25, 30], "1078": 2, "1076": 2, "additional_variant_field": [2, 70], "1056": 2, "header": [2, 45, 46, 47, 48, 50, 65], "when": [2, 3, 6, 17, 26, 28, 29, 30, 36, 37, 38, 39, 40, 45, 46, 47, 55, 63, 67, 69, 70, 120, 159, 163, 168, 173, 174], "write": [2, 3, 4, 6, 46, 48, 170, 172, 174], "write_vcf": [2, 50, 173], "zarr_to_vcf": [2, 48, 173], "previous": [2, 3], "dataset": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 84, 89, 120, 139, 163, 164, 165, 166, 167, 168, 170], "had": [2, 6], "contain": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 39, 40, 41, 47, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 98, 130, 139, 163, 164, 165, 166, 167, 168, 173], "vcf_header": [2, 48, 50], "attribut": [2, 4, 6, 20, 48, 50, 90, 168, 169, 173, 174], "1021": 2, "1020": 2, "contig": [2, 4, 37, 39, 40, 66, 70, 90, 98, 145, 160, 165, 166, 167, 168, 169, 173, 174], "contig_id": [2, 4, 168, 169], "filter": [2, 4, 6, 45, 46, 47, 59, 168, 170, 174], "filter_id": [2, 4], "duplic": [2, 3, 69], "inform": [2, 3, 4, 6, 7, 9, 19, 21, 22, 28, 29, 37, 39, 40, 45, 46, 47, 52, 58, 65, 165, 166, 167, 168, 173, 174], "which": [2, 3, 4, 6, 10, 21, 23, 25, 27, 28, 29, 30, 35, 36, 38, 41, 44, 45, 46, 47, 49, 51, 52, 56, 61, 62, 63, 65, 66, 69, 73, 75, 76, 78, 80, 82, 120, 130, 133, 166, 168, 170, 171, 172, 173, 174], "now": [2, 3, 4, 6, 56, 168, 172, 173], "remov": [2, 4, 6, 23, 25, 26, 36, 38, 52, 57, 66, 169], "futur": [2, 3, 6, 172, 173], "releas": [2, 3, 4, 6, 171, 172, 174], "1054": 2, "1035": 2, "paramet": [2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 173, 174], "founder_indic": [2, 63], "pedigree_kinship": [2, 6], "instead": [2, 6, 36, 38, 63], "founder_kinship": [2, 63], "expect": [2, 4, 6, 60, 61, 63, 133, 134, 137, 173, 174], "full": [2, 4, 6, 28, 29, 39, 40, 41, 42, 59, 61, 63, 168, 173, 174], "kinship": [2, 6, 10, 59, 61, 62, 63, 96, 125, 135, 137, 172], "founder": [2, 6, 61, 62, 63, 69], "ignor": [2, 4, 6, 29, 45, 46, 48, 49, 55, 56, 63, 66, 67, 98, 163, 168], "1075": 2, "1061": 2, "scale": [2, 4, 6, 10, 28, 29, 111, 168, 170, 173, 174], "number": [2, 3, 4, 6, 15, 16, 17, 18, 19, 25, 27, 32, 33, 34, 36, 38, 41, 44, 45, 46, 47, 59, 63, 65, 66, 67, 69, 70, 71, 103, 104, 105, 106, 107, 120, 140, 143, 146, 152, 153, 154, 155, 156, 163, 166, 167, 168, 173, 174], "1028": 2, "1026": 2, "1027": 2, "import": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 28, 29, 30, 31, 35, 37, 39, 40, 48, 52, 55, 56, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 170, 173, 174], "much": [2, 4, 6, 36, 37, 38, 174], "faster": [2, 4, 63, 173, 174], "due": [2, 3, 6, 60, 168, 174], "defer": 2, "compil": [2, 168, 173], "1039": [2, 3], "939": 2, "wa": [2, 3, 4, 25, 35, 38, 172], "output": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 43, 45, 46, 47, 48, 50, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 173, 174], "file": [2, 3, 4, 6, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 65, 68, 170, 172, 173], "temp_chunk_length": [2, 36, 45, 46, 174], "chunk": [2, 4, 6, 7, 9, 21, 22, 35, 36, 37, 38, 39, 40, 43, 45, 46, 47, 48, 58, 60, 68, 169, 170, 171, 172, 173], "ha": [2, 3, 4, 6, 14, 17, 36, 44, 61, 62, 63, 69, 70, 168, 173, 174], "been": [2, 3, 4, 6, 17, 44, 48, 52, 61, 166, 173], "so": [2, 3, 4, 6, 25, 36, 38, 44, 45, 46, 47, 48, 61, 62, 63, 66, 70, 165, 168, 169, 173, 174], "fail": [2, 37], "zerodivisionerror": 2, "1069": 2, "1068": 2, "correct": [2, 3, 6, 10, 168], "mix": [2, 13, 18, 26, 32, 61, 62, 63, 67, 69, 77, 84, 163, 170], "ploidi": [2, 4, 6, 13, 14, 18, 25, 27, 31, 32, 33, 34, 40, 41, 45, 46, 47, 52, 59, 60, 61, 62, 63, 65, 67, 69, 70, 75, 76, 77, 80, 84, 86, 113, 120, 157, 163, 168, 169, 170, 173], "display_genotyp": [2, 4, 10, 11, 12, 13, 15, 16, 17, 18, 23, 30, 31, 69, 168, 169, 173], "1030": 2, "571": 2, "813": 2, "801": 2, "pedigre": [2, 10, 20, 28, 29, 40, 41, 57, 60, 61, 62, 63, 64, 69, 133, 134, 135, 136, 137, 138], "parent": [2, 6, 20, 57, 60, 61, 62, 63, 64, 69, 94, 95, 119, 120], "child": 2, "pedigree_inbreed": 2, "pedigree_inverse_kinship": 2, "786": 2, "implement": [2, 4, 6, 8, 24, 26, 59, 61, 168, 172], "calcul": [2, 4, 6, 7, 9, 17, 21, 22, 27, 28, 29, 30, 35, 44, 52, 55, 56, 57, 58, 60, 61, 62, 113, 135, 136, 157, 163, 164, 165, 166, 167], "vanraden": [2, 25], "genom": [2, 25, 28, 29, 40, 44, 45, 46, 47, 49, 60, 61, 63, 66, 120, 125, 126, 133, 164, 166, 168, 170, 172], "903": [2, 4], "874": 2, "cohort": [2, 7, 8, 9, 12, 16, 21, 22, 26, 55, 58, 87, 88, 101, 114, 115, 116, 117, 118, 121, 123, 124, 131, 132, 170], "sum": [2, 4, 6, 10, 52, 69, 120, 168, 173], "mean": [2, 3, 4, 6, 8, 25, 36, 38, 45, 46, 47, 49, 55, 58, 66, 166, 168, 174], "867": 2, "730": 2, "toggl": 2, "environ": [2, 170, 173, 174], "variabl": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 45, 46, 47, 48, 51, 52, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 163, 164, 165, 166, 167, 168, 170, 174], "sgkit_disable_numba_cach": [2, 173], "870": 2, "869": 2, "window_by_genom": [2, 168], "whole": [2, 6, 54, 66, 164, 168, 174], "statist": [2, 3, 4, 7, 8, 9, 21, 22, 24, 25, 26, 55, 58, 66, 67, 70, 115, 116, 117, 118, 122, 132, 151, 163, 164, 165, 166, 167, 168, 172, 173, 174], "945": 2, "893": 2, "window_by_interv": 2, "creat": [2, 3, 4, 6, 37, 48, 64, 65, 168, 170, 173, 174], "window": [2, 7, 8, 9, 21, 22, 51, 52, 55, 58, 114, 115, 116, 117, 118, 121, 123, 124, 131, 132, 160, 161, 162, 164, 165, 166, 167, 170, 173, 174], "arbitrari": [2, 4, 165], "interv": [2, 31, 90, 91, 92, 165, 168, 173], "974": 2, "contig_length": [2, 4], "found": [2, 3, 6, 25], "946": 2, "464": 2, "export": [2, 170, 173], "953": 2, "924": 2, "auto_rechunk": [2, 68], "save_dataset": [2, 39, 169, 173], "automat": [2, 3, 6, 18, 27, 29, 66, 68, 173], "rechunk": [2, 26, 36, 38, 43, 46, 56, 68, 169, 173, 174], "befor": [2, 3, 4, 7, 8, 9, 21, 22, 55, 58, 63, 68, 168, 173], "save": [2, 68, 170, 173], "disk": [2, 36, 38, 39, 42, 46, 47, 168, 174], "necessari": [2, 3, 4, 23, 26, 37, 68, 173, 174], "requir": [2, 3, 6, 8, 25, 28, 30, 38, 59, 60, 61, 62, 63, 68, 69, 168, 169, 173, 174], "equal": [2, 6, 14, 27, 36, 40, 41, 44, 46, 47, 61, 62, 63, 64, 166, 169, 174], "988": 2, "981": 2, "gene": [2, 69], "\u03b5": [2, 24], "set": [2, 4, 6, 14, 25, 26, 27, 36, 38, 39, 40, 41, 42, 45, 46, 47, 49, 52, 54, 56, 66, 112, 166, 168, 169, 170, 173, 174], "associ": [2, 4, 26, 66, 149, 168, 172], "analysi": [2, 4, 6, 23, 25, 26, 46, 47, 59, 69, 168, 172, 174], "975": 2, "692": 2, "count_variant_genotyp": [2, 27, 163], "occurr": [2, 4, 11, 12, 15, 16, 17, 71, 72, 88, 140, 141, 143, 163], "each": [2, 3, 4, 6, 11, 12, 13, 15, 16, 17, 18, 20, 25, 26, 27, 32, 33, 34, 44, 45, 46, 49, 51, 56, 57, 60, 61, 62, 63, 64, 66, 69, 70, 71, 72, 73, 75, 77, 78, 79, 80, 81, 82, 85, 88, 101, 109, 110, 113, 120, 133, 140, 141, 145, 146, 147, 149, 151, 157, 160, 163, 165, 166, 167, 168, 169, 173, 174], "possibl": [2, 3, 4, 6, 18, 66, 74, 142, 146, 168, 170, 173, 174], "911": 2, "1002": 2, "927": 2, "802": 2, "The": [2, 3, 4, 8, 10, 18, 19, 21, 23, 25, 26, 27, 28, 29, 30, 35, 36, 38, 40, 43, 44, 45, 46, 47, 48, 49, 50, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 67, 69, 70, 100, 101, 102, 103, 104, 105, 106, 107, 119, 120, 128, 130, 141, 142, 143, 144, 146, 148, 152, 153, 154, 155, 156, 158, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174], "count_a1": [2, 40], "read_plink": [2, 39, 173], "true": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 74, 163, 164, 165, 166, 167, 168, 173], "fals": [2, 4, 6, 25, 28, 29, 35, 37, 39, 40, 45, 46, 47, 61, 62, 63, 64, 66, 68, 69, 164, 166, 167, 168, 169, 173], "furthermor": [2, 174], "longer": 2, "clear": [2, 3], "how": [2, 3, 4, 5, 6, 48, 63, 168, 170, 173, 174], "behav": [2, 168], "952": 2, "947": 2, "dosag": [2, 4, 6, 25, 26, 36, 38, 51, 52, 66, 74, 174], "specif": [2, 3, 4, 40, 41, 45, 46, 47, 59, 70, 79, 146, 168, 170, 171, 172, 174], "all": [2, 3, 4, 6, 8, 10, 14, 18, 25, 28, 29, 30, 33, 34, 36, 38, 39, 40, 41, 42, 48, 52, 55, 56, 58, 60, 61, 62, 63, 64, 66, 69, 70, 81, 89, 113, 120, 122, 129, 139, 143, 157, 163, 168, 169, 173, 174], "refer": [2, 3, 4, 10, 18, 19, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 45, 50, 59, 61, 62, 63, 66, 67, 69, 84, 106, 107, 112, 146, 155, 156, 158, 163, 168, 170, 173, 174], "have": [2, 3, 4, 6, 20, 25, 26, 27, 28, 29, 44, 45, 46, 47, 48, 49, 52, 60, 61, 62, 63, 65, 66, 69, 166, 168, 169, 172, 173, 174], "replac": [2, 6, 23, 25, 31, 64, 76, 119, 168, 173], "call_dosage_spec": [2, 25, 26, 37, 51, 52, 66], "includ": [2, 3, 4, 6, 7, 18, 28, 29, 35, 36, 38, 39, 40, 41, 42, 48, 50, 51, 57, 64, 69, 120, 168, 172, 173, 174], "encod": [2, 4, 6, 36, 38, 45, 46, 47, 61, 63, 74, 79, 84, 119, 168, 171, 172, 174], "addition": [2, 26], "ld_matrix": [2, 52, 54], "ld_prune": 2, "call_dosag": [2, 4, 6, 25, 51, 52, 66, 74], "995": [2, 6, 168], "875": 2, "variant_genotype_count_spec": [2, 18, 27], "follow": [2, 3, 4, 6, 8, 14, 24, 25, 28, 29, 36, 37, 39, 40, 41, 42, 45, 46, 47, 50, 56, 61, 62, 63, 65, 66, 67, 69, 70, 79, 146, 163, 164, 165, 166, 167, 168, 173, 174], "order": [2, 3, 4, 6, 14, 18, 23, 25, 28, 54, 57, 63, 146, 173], "e": [2, 6, 18, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 51, 52, 56, 60, 61, 63, 67, 69, 74, 108, 109, 110, 163, 168, 173, 174], "homozyg": [2, 4, 6, 27, 67, 105, 106, 107, 146, 154, 155, 156, 163], "heterozyg": [2, 4, 6, 27, 67, 104, 146, 153, 163, 168], "altern": [2, 4, 6, 19, 25, 27, 45, 46, 47, 65, 67, 74, 79, 105, 146, 154, 163, 168, 169, 173], "biallel": [2, 4, 6, 25, 27, 41, 59, 79, 146, 173], "diploid": [2, 4, 6, 8, 19, 25, 27, 31, 36, 37, 38, 41, 59, 60, 61, 62, 63, 69, 146, 174], "hardy_weinberg_test": [2, 4, 169], "pars": [2, 174], "933": 2, "compress": [2, 36, 38, 44, 45, 46, 47, 48, 49, 168, 170], "937": 2, "925": 2, "ensur": [2, 3, 6], "excess": [2, 54], "dimens": [2, 4, 6, 7, 9, 10, 18, 21, 22, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 43, 45, 46, 47, 48, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 69, 119, 120, 161, 162, 164, 165, 166, 167, 168, 169, 173, 174], "943": 2, "asv": [2, 3], "benchmark": [2, 170, 174], "976": 2, "978": 2, "837": 2, "836": 2, "vlenutf8": 2, "doubl": [2, 3, 61, 63], "852": [2, 4], "785": 2, "input": [2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 45, 46, 47, 48, 49, 50, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 69, 163, 164, 165, 166, 167, 173, 174], "weir_goudet_beta": [2, 6], "865": 2, "861": 2, "get_region_start": 2, "work": [2, 3, 4, 168, 170, 172, 174], "colon": 2, "dash": 2, "d": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 41, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 121, 163, 164, 165, 166, 167, 168, 169, 173, 174], "laub": 2, "883": 2, "882": 2, "hypothesi": 2, "test": [2, 4, 6, 23, 24, 27, 66, 147, 170, 173], "972": 2, "bug": 3, "report": [3, 4, 26], "fix": [3, 25, 32, 45, 46, 47, 65, 168, 173, 174], "improv": [3, 6, 25, 168, 174], "enhanc": 3, "idea": [3, 174], "welcom": 3, "resourc": [3, 168, 173], "best": [3, 6, 66, 99], "part": [3, 44, 45, 46, 49, 174], "came": 3, "dask": [3, 4, 6, 37, 39, 40, 46, 47, 48, 56, 65, 168, 169, 170, 173, 174], "guidelin": [3, 168], "convers": [3, 46, 47, 65, 173], "about": [3, 4, 6, 52, 168, 170, 174], "happen": 3, "place": [3, 48, 168, 174], "github": [3, 4, 45, 46, 47, 65], "tracker": 3, "around": [3, 6, 53, 68, 166, 174], "new": [3, 4, 6, 23, 48, 64, 168, 170, 172, 173], "featur": [3, 168, 173, 174], "question": [3, 6, 172], "do": [3, 6, 28, 29, 66, 168, 170, 174], "x": [3, 4, 6, 56, 133, 168, 169, 173], "what": 3, "wai": [3, 168, 173, 174], "y": [3, 4, 133], "genet": [3, 4, 6, 10, 24, 25, 26, 27, 28, 29, 51, 52, 59, 61, 62, 63, 66, 69, 123, 124, 172, 174], "tend": 3, "higher": [3, 46, 47, 168, 173, 174], "theme": 3, "detail": [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 45, 50, 55, 57, 58, 59, 66, 67, 69, 163, 164, 165, 166, 167, 168, 170, 173], "pull": 3, "request": [3, 4, 6, 173, 174], "maintain": 3, "few": [3, 4, 6, 168, 170, 173, 174], "host": [3, 173], "dev": [3, 4, 169, 173], "organ": 3, "primari": [3, 6, 168], "sever": [3, 6, 59, 74, 168, 173], "other": [3, 6, 7, 25, 48, 56, 60, 61, 62, 63, 70, 74, 168, 170, 172, 174], "differ": [3, 4, 6, 168, 173, 174], "compon": [3, 4, 24, 59, 108, 109, 110, 111, 112], "A": [3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 73, 75, 77, 78, 80, 81, 82, 101, 163, 164, 165, 166, 167, 168, 169, 173, 174], "exhaust": 3, "list": [3, 4, 43, 45, 46, 47, 66, 168, 170, 173, 174], "main": [3, 168, 174], "algorithm": [3, 38, 54, 56, 168, 172, 174], "can": [3, 4, 6, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 56, 61, 62, 63, 68, 74, 111, 120, 164, 168, 169, 173, 174], "challeng": 3, "first": [3, 4, 6, 19, 24, 25, 28, 29, 30, 37, 39, 40, 43, 45, 46, 47, 59, 64, 65, 84, 168, 169, 173, 174], "fortun": [3, 6], "good": [3, 45, 46, 49, 56, 170, 174], "materi": [3, 54, 169], "exist": [3, 4, 6, 37, 173], "internet": 3, "repeat": [3, 7, 8, 9, 12, 16, 21, 22, 55, 58, 168], "here": [3, 4, 6, 168, 173, 174], "we": [3, 4, 6, 168, 172, 173, 174], "panda": [3, 4, 6, 168, 169, 170, 173], "link": 3, "subject": [3, 4, 6], "http": [3, 4, 6, 37, 38, 39, 40, 45, 46, 47, 65, 66, 173], "pydata": [3, 168], "org": [3, 6, 37, 39, 40, 66], "stabl": 3, "html": [3, 37, 39, 40, 66], "track": [3, 173, 174], "known": [3, 6, 10, 57, 63, 124, 166], "potenti": [3, 6, 168], "identifi": [3, 4, 6, 26, 37, 40, 41, 57, 69, 94, 102, 148], "rais": [3, 6, 8, 13, 18, 20, 25, 27, 28, 29, 40, 41, 44, 45, 46, 47, 51, 52, 54, 57, 59, 60, 61, 62, 63, 66, 67, 69, 163, 166, 173, 174], "start": [3, 4, 6, 48, 50, 91, 161, 164, 165, 166, 167, 170, 172, 174], "public": 3, "look": [3, 4, 6, 170, 174], "introductori": 3, "get": [3, 6, 52, 170], "out": [3, 4, 46, 48, 49, 66, 98, 99, 168, 169, 173], "label": [3, 56, 168], "familiar": 3, "some": [3, 4, 6, 145, 164, 165, 166, 167, 168, 169, 173, 174], "parallel": [3, 45, 46, 49, 168, 173, 174], "assum": [3, 10, 19, 28, 29, 32, 60, 61, 62, 63, 139, 174], "sure": 3, "cover": [3, 6, 174], "plan": 3, "produc": [3, 6, 43, 66, 70, 168, 174], "assign": [3, 18, 27, 168, 169], "yourself": 3, "indic": [3, 6, 28, 29, 35, 51, 57, 61, 62, 63, 73, 74, 75, 77, 78, 79, 80, 81, 82, 84, 95, 101, 113, 130, 157, 168, 173, 174], "In": [3, 6, 48, 108, 145, 168, 169, 173, 174], "mention": 3, "relat": [3, 6, 10, 59, 63, 96, 168, 172], "fork": 3, "clone": [3, 61, 62, 63], "com": [3, 4, 6], "usernam": 3, "made": [3, 14], "submit": [3, 173], "pip": [3, 168, 173, 174], "cd": 3, "r": [3, 4, 6, 25, 27, 28, 29, 59, 66], "txt": [3, 4, 6], "nvidia": 3, "gpu": [3, 56, 168], "need": [3, 4, 6, 25, 37, 38, 40, 45, 46, 47, 65, 168, 169, 173, 174], "configur": [3, 174], "properli": 3, "cudatoolkit": 3, "instruct": [3, 173, 174], "same": [3, 4, 6, 7, 19, 21, 28, 29, 36, 63, 66, 167, 168, 173, 174], "also": [3, 4, 6, 36, 37, 38, 40, 45, 46, 49, 56, 61, 62, 63, 64, 111, 119, 120, 124, 145, 166, 168, 169, 172, 173, 174], "pre": 3, "commit": 3, "enforc": 3, "pytest": 3, "directori": [3, 4, 36, 38, 39, 42, 43, 45, 46, 47, 50, 53, 68], "similar": [3, 4, 173], "languag": 3, "style": [3, 4], "action": 3, "ci": 3, "servic": 3, "everi": [3, 56, 168, 174], "push": 3, "coverag": 3, "build": [3, 168], "emploi": 3, "extens": [3, 4, 39, 40, 41, 42], "both": [3, 6, 25, 26, 44, 45, 46, 49, 60, 61, 63, 166, 168, 170, 173, 174], "todai": 3, "must": [3, 6, 8, 13, 14, 15, 18, 25, 26, 27, 28, 29, 32, 33, 34, 36, 38, 39, 40, 41, 42, 44, 45, 46, 51, 52, 59, 61, 62, 63, 66, 67, 69, 70, 89, 90, 119, 120, 139, 163, 165, 166, 169, 174], "100": [3, 4, 36, 48, 66, 168, 169, 173, 174], "accept": [3, 172, 174], "measur": [3, 166, 167, 168], "local": [3, 4, 6, 36, 173, 174], "machin": [3, 48, 173, 174], "cov": 3, "written": [3, 4, 46, 48, 50], "htmlcov": 3, "show": [3, 4, 5, 6, 38, 48, 168, 173, 174], "line": [3, 48, 50, 173], "suit": 3, "live": 3, "filenam": [3, 173], "test_": 3, "modul": [3, 173], "py": [3, 6, 173], "underscor": 3, "group": [3, 4, 168], "def": [3, 4, 173], "test_foo__accepts_empty_input": 3, "test_foo__accepts_str": 3, "user": [3, 45, 74, 168, 170], "face": 3, "numpydoc": 3, "section": [3, 45, 46, 47, 65, 174], "explanatori": 3, "prose": 3, "ad": [3, 6, 24, 26, 39, 40, 41, 42, 48, 168, 170], "thei": [3, 4, 6, 26, 41, 56, 168, 173, 174], "onli": [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 52, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 168, 169, 173, 174], "hint": [3, 44], "rst": 3, "them": [3, 4, 6, 168, 173, 174], "access": [3, 4, 6, 168, 170, 174], "reproduc": 3, "valuabl": 3, "importantli": [3, 6], "common": [3, 4, 6, 59, 145, 168, 169, 172], "trump": 3, "case": [3, 6, 21, 31, 40, 41, 45, 46, 47, 48, 65, 120, 168, 173, 174], "take": [3, 4, 6, 45, 46, 49, 168, 174], "preced": 3, "over": [3, 37, 45, 46, 49, 165, 166, 167, 168, 170, 174], "space": [3, 38, 166, 168, 174], "To": [3, 4, 6, 7, 8, 9, 21, 22, 55, 56, 58, 168, 173, 174], "skip": [3, 25, 30, 174], "comment": [3, 4, 6, 168, 169, 173], "after": [3, 4, 6, 45, 46, 173], "becaus": [3, 6, 36, 48, 168, 173, 174], "setup": [3, 173], "cfg": 3, "succe": 3, "chang": [3, 4, 6, 45, 46, 47], "pass": [3, 4, 20, 23, 24, 36, 37, 39, 40, 49, 53, 56, 68, 173, 174], "It": [3, 4, 6, 48, 168, 173, 174], "tool": [3, 48, 168, 170, 173], "black": [3, 4], "flake8": 3, "consist": [3, 6, 173, 174], "isort": 3, "mypi": 3, "static": 3, "manual": [3, 6, 45, 173, 174], "adher": 3, "without": [3, 4, 6, 25, 31, 38, 48, 66, 119, 164, 166, 167, 168, 169, 173, 174], "etc": [3, 66, 173], "omit": [3, 36, 38, 48, 56, 81], "current": [3, 7, 8, 9, 21, 22, 26, 27, 28, 29, 37, 40, 45, 46, 49, 58, 60, 174], "rebas": 3, "squash": 3, "merg": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 168], "strategi": 3, "certain": [3, 38], "practic": [3, 6, 168], "life": 3, "easier": [3, 4, 53, 68, 168, 169, 173], "try": [3, 173], "isol": [3, 168], "singl": [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 40, 43, 44, 46, 49, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 79, 119, 163, 164, 165, 166, 167, 168, 173, 174], "guarante": [3, 174], "speedi": 3, "meaning": 3, "small": [3, 4, 30, 46, 47, 169, 173, 174], "again": [3, 4, 173], "buggi": 3, "veri": [3, 4, 45, 46, 47, 51, 52, 173, 174], "handi": [3, 173], "interact": [3, 168], "runtim": [3, 46, 47], "one": [3, 4, 6, 14, 25, 26, 29, 40, 41, 44, 47, 48, 61, 62, 63, 74, 168, 173, 174], "don": [3, 6, 172, 174], "t": [3, 4, 6, 25, 26, 28, 29, 39, 40, 151, 168, 169, 172, 173, 174], "forget": 3, "keep": 3, "exclud": [3, 59], "minimum": [3, 173], "sometim": [3, 6, 168, 174], "unavoid": 3, "conflict": 3, "manag": [3, 168, 173], "conda": [3, 168, 173, 174], "forg": [3, 168], "feedstock": 3, "There": [3, 4, 168, 173, 174], "night": 3, "against": [3, 4, 66], "branch": [3, 58, 132], "kei": [3, 20, 36, 45, 46, 47, 56, 65, 174], "upstream": [3, 173], "find": [3, 44, 52, 170, 174], "break": [3, 174], "would": [3, 6, 168, 173, 174], "affect": [3, 6], "problem": 3, "librari": [3, 4, 6, 20, 168, 172, 174], "sphinx": 3, "restructuredtext": 3, "markup": 3, "graphviz": [3, 20], "dot": 3, "execut": [3, 168], "result": [3, 4, 6, 13, 17, 25, 35, 36, 38, 39, 40, 52, 56, 57, 61, 62, 63, 65, 66, 69, 70, 98, 110, 119, 168, 170, 173, 174], "end": [3, 6, 168, 174], "up": [3, 48, 64, 173, 174], "_build": 3, "edit": [3, 4, 26], "warn": [3, 4, 173], "clean": 3, "sphinxopt": 3, "w": [3, 4, 24, 28, 29, 69, 173], "go": 3, "n": [3, 4, 6, 25, 26, 27, 28, 29, 56, 71, 72, 74, 76, 77, 78, 79, 81, 84, 85, 88, 89, 93, 94, 95, 97, 98, 99, 108, 110, 119, 120, 125, 126, 129, 130, 131, 133, 137, 139, 140, 145, 146, 159, 168], "airspe": 3, "veloc": 3, "micro": 3, "via": [3, 69, 168, 173], "itself": 3, "recip": 3, "defin": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 45, 46, 47, 51, 52, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 74, 90, 108, 111, 146, 163, 165, 166, 167, 168, 170, 173], "conf": 3, "json": [3, 4], "readthedoc": [3, 38, 66], "en": [3, 37, 38, 39, 40, 66], "writing_benchmark": 3, "upload": 3, "seen": [3, 168], "site": [3, 31], "config": [3, 56, 173], "publish": [3, 6], "v": [3, 4, 6, 28, 29, 59], "browser": 3, "server": 3, "preview": 3, "roughli": [3, 44, 66, 174], "arch": 3, "x86_64": 3, "cpu": [3, 56, 173], "intel": 3, "xeon": 3, "platinum": 3, "8272cl": 3, "2": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 40, 41, 45, 46, 47, 51, 52, 55, 56, 59, 60, 61, 62, 63, 65, 66, 69, 70, 73, 74, 78, 79, 81, 84, 85, 86, 89, 94, 95, 96, 98, 99, 108, 111, 112, 115, 116, 117, 118, 119, 120, 121, 122, 124, 125, 126, 127, 128, 129, 130, 131, 133, 135, 136, 137, 138, 139, 140, 141, 142, 146, 149, 150, 151, 164, 166, 167, 168, 169, 170, 173, 174], "60ghz": 3, "fv": 3, "az183": 3, "669": [3, 4], "num_cpu": 3, "o": [3, 26, 27, 90, 94, 102, 142, 148, 173], "linux": [3, 173], "5": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 16, 21, 22, 25, 27, 28, 29, 30, 35, 52, 55, 56, 58, 59, 60, 62, 63, 66, 69, 166, 167, 168, 169, 171, 172, 173, 174], "4": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 31, 45, 46, 47, 48, 52, 55, 56, 59, 61, 62, 63, 65, 69, 97, 132, 166, 167, 168, 169, 173, 174], "azur": [3, 173], "ram": 3, "7121276": 3, "1": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 40, 41, 45, 46, 47, 48, 51, 55, 56, 57, 59, 60, 61, 62, 63, 64, 65, 66, 69, 70, 78, 79, 84, 89, 90, 91, 92, 93, 97, 99, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 113, 133, 134, 139, 143, 144, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 164, 166, 167, 168, 169, 170, 173, 174], "abov": [3, 4, 6, 36, 38, 51, 52, 56, 168, 173], "command": [3, 4, 173], "ye": 3, "doe": [3, 4, 6, 7, 9, 13, 18, 21, 22, 37, 48, 58, 61, 62, 63, 65, 66, 67, 69, 98, 163, 174], "slightli": [3, 4, 6, 51, 52], "could": [3, 6], "sai": 3, "30ghz": 3, "less": [3, 6, 14, 32, 44, 48, 59, 145, 169, 174], "huge": 3, "deviat": 3, "though": [3, 6, 168, 170], "unless": [3, 17], "custom": [3, 74, 168], "henc": [3, 6, 23, 174], "minor": [3, 6, 51, 52, 59], "consum": 3, "pinch": 3, "salt": 3, "approv": 3, "least": [3, 6, 10, 14, 51, 52, 61, 62, 63, 66, 98], "mergifi": 3, "autom": 3, "flow": 3, "committ": 3, "decid": [3, 56], "topic": [3, 6], "mai": [3, 6, 10, 25, 28, 29, 37, 38, 44, 45, 46, 47, 49, 57, 61, 62, 63, 66, 69, 119, 130, 145, 166, 168, 169, 170, 173, 174], "understand": [3, 173, 174], "histori": 3, "behind": [3, 4, 174], "choic": [3, 4], "within": [3, 6, 25, 31, 35, 37, 40, 41, 55, 57, 61, 62, 63, 65, 70, 77, 119, 120, 139, 165, 166, 168, 170, 173, 174], "far": [3, 4], "debat": 3, "whether": [3, 36, 37, 38, 39, 40, 51, 66, 70], "object": [3, 4, 6, 19, 36, 48, 50, 168, 169, 173, 174], "put": 3, "layer": [3, 4, 6], "encapsul": 3, "16": [3, 4, 24, 28, 29, 56, 59, 168, 169, 173, 174], "78": [3, 4], "bring": 3, "stricter": 3, "43": [3, 168, 173], "124": [3, 69], "276": 3, "295": [3, 29], "saniti": 3, "effici": [3, 6, 17, 25, 26, 28, 29, 30, 61, 66, 168, 174], "why": [3, 4], "those": [3, 6, 18, 25, 51, 52, 61, 62, 63, 69, 70, 94, 119, 120, 168, 170, 173], "61": [3, 4, 168], "97": [3, 4, 168], "propos": 3, "243": 3, "learn": [3, 24, 26, 173], "effect": [3, 6, 14, 24, 26, 28, 29, 66, 98, 168], "114": 3, "348": 3, "init": 3, "accommod": 3, "__all__": 3, "declar": [3, 4, 173], "decis": 3, "251": 3, "notebook": [4, 5, 6, 173], "port": 4, "hail": [4, 170], "demonstr": [4, 6, 168, 173], "run": [4, 26, 38, 46, 47, 56, 168, 173], "wide": [4, 6, 172], "snp": [4, 6, 24, 59], "reader": 4, "encourag": 4, "alongsid": 4, "background": 4, "motiv": [4, 6], "step": [4, 6, 8, 28, 29, 46, 56, 166, 167, 168, 173, 174], "note": [4, 6, 23, 27, 38, 40, 45, 46, 47, 52, 65, 70, 168, 173, 174], "exactli": [4, 44, 174], "still": [4, 6, 23, 170, 174], "its": [4, 6, 25, 61, 63, 64, 69, 168, 173, 174], "api": [4, 6, 37, 39, 40, 56, 168, 169, 170], "backward": [4, 6], "compat": [4, 6, 59, 168], "sg": [4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 28, 29, 30, 31, 35, 52, 55, 57, 58, 61, 62, 63, 69, 164, 166, 167, 168, 169, 173, 174], "standard": [4, 6, 44, 48, 66, 168, 173, 174], "displai": [4, 19, 20, 168, 173], "np": [4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 52, 55, 56, 58, 66, 69, 166, 168, 169, 173, 174], "pd": [4, 6], "xr": [4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 28, 29, 35, 55, 58, 60, 64, 168], "set_opt": 4, "display_expand_attr": 4, "display_expand_data_var": 4, "20mb": [4, 45, 46, 49], "portion": 4, "pathlib": [4, 6], "path": [4, 6, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 65, 68], "1kg": [4, 174], "bgz": [4, 174], "respons": [4, 6], "googleapi": [4, 6], "wb": [4, 6], "f": [4, 6, 28, 29, 58, 61, 72, 74, 83, 85, 88, 96, 97, 98, 99, 100, 108, 109, 110, 111, 112, 114, 115, 116, 117, 118, 119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 141, 144, 147, 150, 159, 169, 173, 174], "content": [4, 6, 40, 66], "tbi": [4, 44, 45, 46, 47, 49, 174], "next": [4, 6], "filesystem": [4, 174], "vcz": 4, "bash": [4, 173], "explod": 4, "forc": [4, 168], "icf": 4, "mkschema": 4, "schema": 4, "hand": 4, "scan": [4, 172], "00": [4, 56, 146, 173], "bcf_hdr_check_san": 4, "pl": 4, "g": [4, 6, 25, 28, 29, 36, 37, 38, 44, 45, 46, 47, 51, 52, 60, 61, 62, 63, 67, 69, 74, 79, 163, 168, 169, 174], "57file": 4, "10": [4, 6, 10, 13, 19, 45, 46, 47, 52, 56, 66, 164, 166, 167, 168, 169, 170, 173, 174], "9k": 4, "var": 4, "50": [4, 6, 24, 28, 29, 66, 168, 169, 173], "21": [4, 6, 56, 166, 168, 169, 173, 174], "495var": 4, "263": 4, "07": 4, "34kvar": 4, "477": 4, "06": [4, 24, 66], "63kvar": 4, "6": [4, 6, 10, 13, 24, 25, 52, 56, 58, 62, 63, 166, 167, 168, 169, 170, 173, 174], "691": 4, "05": [4, 13, 25], "77kvar": 4, "8": [4, 6, 10, 13, 59, 166, 167, 168, 169, 170, 173, 174], "01": [4, 6, 28, 56, 59, 146, 171], "85kvar": 4, "02k": 4, "02": [4, 56, 146], "17": [4, 62, 168, 169, 173], "559var": 4, "11": [4, 6, 25, 56, 146, 168, 169, 173], "24k": 4, "14": [4, 56, 168, 169, 173], "674var": 4, "13": [4, 56, 168, 169, 173], "46k": 4, "12": [4, 6, 56, 146, 166, 168, 169, 173, 174], "783var": 4, "15": [4, 168, 169, 173], "67k": 4, "885var": 4, "82k": 4, "03": [4, 56], "546var": 4, "19": [4, 13, 66, 168, 169, 173], "03k": 4, "623var": 4, "25k": 4, "698var": 4, "23": [4, 56, 168, 169, 173, 174], "776var": 4, "24": [4, 56, 168, 170, 173], "64k": 4, "04": [4, 56, 173], "561var": 4, "26": [4, 168, 173], "78k": 4, "511var": 4, "28": [4, 168, 173], "00k": 4, "573var": 4, "29": [4, 168, 173], "15k": 4, "496var": 4, "31": [4, 56, 168, 173], "37k": 4, "555var": 4, "33": [4, 56, 168, 173], "59k": 4, "615var": 4, "35": [4, 13, 63, 168, 173], "666var": 4, "36": [4, 168, 173], "93k": 4, "527var": 4, "38": [4, 168, 173], "16k": 4, "584var": 4, "40": [4, 166, 168, 173], "38k": 4, "642var": 4, "42": [4, 168, 173], "53k": 4, "08": [4, 171], "521var": 4, "44": [4, 13, 168, 173], "76k": 4, "576var": 4, "46": [4, 168, 173], "98k": 4, "09": 4, "632var": 4, "47": [4, 26, 168, 173], "14k": 4, "532var": 4, "49": [4, 168, 173], "586var": 4, "51": [4, 168, 173], "52k": 4, "472var": 4, "53": [4, 168], "75k": 4, "54": [4, 168], "92k": 4, "557var": 4, "56": [4, 168], "08k": 4, "500var": 4, "58": [4, 168], "30k": 4, "551var": 4, "59": [4, 168], "45k": 4, "581var": 4, "60k": 4, "62": [4, 168], "534var": 4, "64": [4, 29, 168], "99k": 4, "66": [4, 168], "7": [4, 6, 10, 13, 36, 38, 45, 46, 47, 56, 62, 63, 167, 168, 169, 170, 173, 174], "13k": 4, "490var": 4, "68": [4, 168], "35k": 4, "541var": 4, "70": 4, "57k": 4, "593var": 4, "71": [4, 28, 29], "74k": 4, "508var": 4, "73": [4, 28, 29], "547var": 4, "74": 4, "07k": 4, "497var": 4, "75": [4, 8, 12, 60, 63, 168], "21k": 4, "466var": 4, "77": 4, "33k": 4, "443var": 4, "79": 4, "55k": 4, "493var": 4, "80": 4, "68k": 4, "448var": 4, "82": 4, "90k": 4, "498var": 4, "83": 4, "450var": 4, "85": 4, "26k": 4, "501var": 4, "86": 4, "39k": 4, "18": [4, 59, 168, 169, 173], "455var": 4, "88": 4, "62k": 4, "505var": 4, "90": [4, 26], "467var": 4, "92": [4, 28, 29], "97k": 4, "514var": 4, "93": [4, 27, 28, 29], "1k": 4, "468var": 4, "95": [4, 168], "3k": 4, "507var": 4, "96": [4, 168], "4k": 4, "20": [4, 13, 38, 56, 168, 169, 173, 174], "465var": 4, "5k": 4, "438var": 4, "98": [4, 59, 168], "6k": 4, "414var": 4, "510var": 4, "2m": 4, "b": [4, 6, 25, 73, 75, 77, 78, 80, 81, 82, 168, 169, 173], "0k": 4, "889kb": 4, "270k": 4, "22": [4, 6, 56, 146, 168, 169, 173, 174], "23mb": 4, "350k": 4, "25": [4, 8, 10, 12, 28, 29, 35, 60, 61, 63, 166, 168, 173], "08mb": 4, "03m": 4, "86mb": 4, "87m": 4, "38mb": 4, "7m": 4, "3mb": 4, "4m": 4, "8mb": 4, "9m": 4, "7mb": 4, "4mb": 4, "finalis": 4, "26karrai": 4, "intermedi": [4, 36, 38, 45, 46, 62, 173, 174], "columnar": [4, 171, 172], "specifi": [4, 8, 17, 25, 27, 28, 29, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 58, 60, 61, 62, 63, 64, 69, 70, 166, 168, 174], "drop": [4, 6, 45, 46, 47, 54, 64, 69, 93, 169], "call_ad": 4, "third": [4, 61, 62, 63, 64, 168, 172], "unknown": [4, 6, 25, 28, 29, 57, 60, 61, 62, 63, 69, 95, 120, 168, 169, 173], "document": [4, 18, 168, 169, 170, 173, 174], "downstream": [4, 38, 46, 47, 164, 165, 166, 167], "oper": [4, 6, 49, 170], "repres": [4, 6, 45, 46, 47, 65, 74, 168, 173, 174], "where": [4, 6, 10, 21, 25, 36, 38, 45, 46, 47, 52, 61, 64, 65, 70, 165, 168, 172, 173, 174], "matrixt": 4, "load_dataset": [4, 42, 45, 50, 169, 173, 174], "ll": 4, "simplest": [4, 168, 173], "thing": 4, "lt": [4, 6], "gt": [4, 6, 173], "28mb": [4, 6], "10879": 4, "284": [4, 26], "84": 4, "coordin": [4, 6, 18, 27, 64, 66, 164, 166, 167, 168, 169, 173, 174], "int8": [4, 168, 169, 173, 174], "6mb": 4, "chunksiz": [4, 6, 168, 169, 173, 174], "10000": [4, 6, 36, 38, 45, 46, 47, 174], "meta": [4, 6, 66, 99, 168, 169, 173, 174], "ndarrai": [4, 6, 20, 24, 56, 64, 69, 168, 169, 173, 174], "call_dp": 4, "call_gq": 4, "call_genotyp": [4, 8, 10, 13, 14, 15, 17, 18, 23, 26, 30, 32, 33, 34, 45, 46, 47, 52, 59, 67, 69, 84, 163, 168, 169, 173, 174], "call_genotype_mask": [4, 14, 23, 25, 59, 80, 168, 169, 174], "bool": [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 169, 174], "call_genotype_phas": [4, 81, 174], "variant_contig": [4, 66, 70, 145, 165, 166, 167, 168, 169, 174], "11kb": [4, 168], "variant_filt": 4, "variant_id": [4, 148, 174], "87kb": 4, "variant_id_mask": [4, 174], "variant_posit": [4, 69, 158, 165, 166, 167, 168, 169, 174], "int32": [4, 174], "44kb": 4, "variant_qu": 4, "float32": [4, 37], "datasetdimens": [4, 6], "10879sampl": 4, "284allel": 4, "2ploidi": 4, "2contig": 4, "84filter": 4, "1coordin": 4, "int8dask": 4, "descript": [4, 45, 46, 47, 65, 66], "byte": [4, 6, 36, 37, 38, 39, 42, 43, 44, 45, 46, 49, 50, 53, 68, 174], "89": 4, "mib": [4, 6], "shape": [4, 6, 7, 9, 11, 12, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 31, 55, 56, 58, 63, 71, 72, 88, 89, 139, 140, 168, 173], "graph": [4, 6, 20, 54, 168, 173], "type": [4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 174], "booldask": 4, "objectdask": 4, "672": 4, "float64dask": 4, "float64": [4, 6, 66, 168, 169], "sample_id": [4, 6, 40, 41, 57, 60, 61, 62, 63, 64, 69, 102, 168, 169, 174], "kib": 4, "variant_allel": [4, 45, 46, 47, 69, 142, 168, 169, 173, 174], "169": 4, "156": 4, "angl": 4, "bracket": 4, "id": [4, 6, 8, 18, 58], "point": [4, 6, 173], "assembli": 4, "statu": 4, "uniqu": [4, 6, 61, 62, 63, 79, 94, 102, 148, 173], "applic": [4, 25, 27, 36, 38, 41, 59, 70, 174], "99": [4, 168, 169], "int32dask": 4, "posit": [4, 44, 56, 63, 77, 91, 92, 158, 161, 162, 164, 165, 166, 167, 168, 174], "39": [4, 168, 173], "float32dask": 4, "phred": 4, "score": [4, 28, 29, 112, 159], "index": [4, 6, 8, 13, 36, 37, 39, 40, 44, 45, 46, 47, 48, 49, 51, 54, 58, 64, 78, 93, 101, 114, 145, 160, 161, 162, 164, 165, 166, 167, 168, 169, 170, 173, 174], "1vcf_header": 4, "fileformat": 4, "vcfv4": [4, 45, 46, 47, 65], "quot": 4, "hailvers": 4, "29fbaeaf265": 4, "dp": [4, 45, 46, 47], "gq": 4, "info": [4, 45, 46, 47, 65], "ac": [4, 45, 46, 47, 65, 173, 174], "af": 4, "float": [4, 14, 24, 26, 27, 28, 29, 48, 51, 52, 59, 66, 70, 74, 147, 150, 168, 174], "baseqranksum": 4, "clippingranksum": 4, "flag": [4, 26, 73, 75, 77, 78, 80, 81, 82, 168], "haplotypescor": 4, "inbreedingcoeff": 4, "mleac": 4, "mleaf": 4, "mq": 4, "mq0": 4, "mqranksum": 4, "qd": 4, "readposranksum": 4, "length": [4, 6, 36, 38, 43, 45, 46, 47, 60, 61, 62, 63, 64, 65, 69, 174], "249250621": 4, "grch37": 4, "243199373": 4, "198022430": 4, "191154276": 4, "180915260": 4, "171115067": 4, "159138663": 4, "146364022": 4, "141213431": 4, "135534747": 4, "135006516": 4, "133851895": 4, "115169878": 4, "107349540": 4, "102531392": 4, "90354753": 4, "81195210": 4, "78077248": 4, "59128983": 4, "63025520": 4, "48129895": 4, "51304566": 4, "155270560": 4, "59373566": 4, "mt": 4, "16569": 4, "gl000207": 4, "4262": 4, "gl000226": 4, "15008": 4, "gl000229": 4, "19913": 4, "gl000231": 4, "27386": 4, "gl000210": 4, "27682": 4, "gl000239": 4, "33824": 4, "gl000235": 4, "34474": 4, "gl000201": 4, "36148": 4, "gl000247": 4, "36422": 4, "gl000245": 4, "36651": 4, "gl000197": 4, "37175": 4, "gl000203": 4, "37498": 4, "gl000246": 4, "38154": 4, "gl000249": 4, "38502": 4, "gl000196": 4, "38914": 4, "gl000248": 4, "39786": 4, "gl000244": 4, "39929": 4, "gl000238": 4, "39939": 4, "gl000202": 4, "40103": 4, "gl000234": 4, "40531": 4, "gl000232": 4, "40652": 4, "gl000206": 4, "41001": 4, "gl000240": 4, "41933": 4, "gl000236": 4, "41934": 4, "gl000241": 4, "42152": 4, "gl000243": 4, "43341": 4, "gl000242": 4, "43523": 4, "gl000230": 4, "43691": 4, "gl000237": 4, "45867": 4, "gl000233": 4, "45941": 4, "gl000204": 4, "81310": 4, "gl000198": 4, "90085": 4, "gl000208": 4, "92689": 4, "gl000191": 4, "106433": 4, "gl000227": 4, "128374": 4, "gl000228": 4, "129120": 4, "gl000214": 4, "137718": 4, "gl000221": 4, "155397": 4, "gl000209": 4, "159169": 4, "gl000218": 4, "161147": 4, "gl000220": 4, "161802": 4, "gl000213": 4, "164239": 4, "gl000211": 4, "166566": 4, "gl000199": 4, "169874": 4, "gl000217": 4, "172149": 4, "gl000216": 4, "172294": 4, "gl000215": 4, "172545": 4, "gl000205": 4, "174588": 4, "gl000219": 4, "179198": 4, "gl000224": 4, "179693": 4, "gl000223": 4, "180455": 4, "gl000195": 4, "182896": 4, "gl000212": 4, "186858": 4, "gl000222": 4, "186861": 4, "gl000200": 4, "187035": 4, "gl000193": 4, "189789": 4, "gl000194": 4, "191469": 4, "gl000225": 4, "211173": 4, "gl000192": 4, "547496": 4, "chrom": [4, 48, 50], "po": [4, 26, 174], "ref": 4, "alt": [4, 173], "qual": 4, "hg00096": 4, "hg00099": 4, "hg00105": 4, "hg00118": 4, "hg00129": 4, "hg00148": 4, "hg00177": 4, "hg00182": 4, "hg00242": 4, "hg00254": 4, "hg00265": 4, "hg00271": 4, "hg00274": 4, "hg00332": 4, "hg00335": 4, "hg00369": 4, "hg00421": 4, "hg00436": 4, "hg00452": 4, "hg00472": 4, "hg00530": 4, "hg00534": 4, "hg00583": 4, "hg00590": 4, "hg00598": 4, "hg00607": 4, "hg00619": 4, "hg00623": 4, "hg00657": 4, "hg00663": 4, "hg00704": 4, "hg00705": 4, "hg00733": 4, "hg00864": 4, "hg00881": 4, "hg01052": 4, "hg01070": 4, "hg01075": 4, "hg01164": 4, "hg01174": 4, "hg01241": 4, "hg01248": 4, "hg01256": 4, "hg01275": 4, "hg01284": 4, "hg01334": 4, "hg01348": 4, "hg01396": 4, "hg01443": 4, "hg01491": 4, "hg01498": 4, "hg01537": 4, "hg01572": 4, "hg01606": 4, "hg01623": 4, "hg01630": 4, "hg01783": 4, "hg01784": 4, "hg01790": 4, "hg01799": 4, "hg01801": 4, "hg01806": 4, "hg01812": 4, "hg01813": 4, "hg01817": 4, "hg01848": 4, "hg01849": 4, "hg01857": 4, "hg01863": 4, "hg01874": 4, "hg01915": 4, "hg01924": 4, "hg01965": 4, "hg01970": 4, "hg01991": 4, "hg02010": 4, "hg02020": 4, "hg02054": 4, "hg02086": 4, "hg02087": 4, "hg02116": 4, "hg02122": 4, "hg02130": 4, "hg02131": 4, "hg02152": 4, "hg02154": 4, "hg02165": 4, "hg02224": 4, "hg02232": 4, "hg02236": 4, "hg02250": 4, "hg02259": 4, "hg02298": 4, "hg02318": 4, "hg02345": 4, "hg02351": 4, "hg02363": 4, "hg02373": 4, "hg02383": 4, "hg02384": 4, "hg02386": 4, "hg02388": 4, "hg02389": 4, "hg02397": 4, "hg02419": 4, "hg02462": 4, "hg02464": 4, "hg02497": 4, "hg02511": 4, "hg02521": 4, "hg02561": 4, "hg02574": 4, "hg02580": 4, "hg02595": 4, "hg02603": 4, "hg02629": 4, "hg02651": 4, "hg02682": 4, "hg02688": 4, "hg02690": 4, "hg02699": 4, "hg02760": 4, "hg02768": 4, "hg02771": 4, "hg02792": 4, "hg02798": 4, "hg02811": 4, "hg02814": 4, "hg02840": 4, "hg02870": 4, "hg02881": 4, "hg02970": 4, "hg02973": 4, "hg03009": 4, "hg03046": 4, "hg03074": 4, "hg03091": 4, "hg03105": 4, "hg03127": 4, "hg03193": 4, "hg03224": 4, "hg03237": 4, "hg03241": 4, "hg03247": 4, "hg03259": 4, "hg03267": 4, "hg03354": 4, "hg03366": 4, "hg03367": 4, "hg03380": 4, "hg03419": 4, "hg03449": 4, "hg03451": 4, "hg03458": 4, "hg03490": 4, "hg03491": 4, "hg03511": 4, "hg03556": 4, "hg03563": 4, "hg03598": 4, "hg03603": 4, "hg03607": 4, "hg03636": 4, "hg03684": 4, "hg03686": 4, "hg03690": 4, "hg03731": 4, "hg03740": 4, "hg03755": 4, "hg03800": 4, "hg03815": 4, "hg03832": 4, "hg03850": 4, "hg03873": 4, "hg03897": 4, "hg03905": 4, "hg03937": 4, "hg03948": 4, "hg03973": 4, "hg04054": 4, "hg04059": 4, "hg04063": 4, "hg04096": 4, "hg04099": 4, "hg04140": 4, "hg04171": 4, "hg04209": 4, "hg04210": 4, "hg04229": 4, "hg04239": 4, "na07347": 4, "na11918": 4, "na11919": 4, "na12045": 4, "na12273": 4, "na12342": 4, "na12414": 4, "na12546": 4, "na12760": 4, "na12878": 4, "na18516": 4, "na18525": 4, "na18534": 4, "na18541": 4, "na18557": 4, "na18565": 4, "na18616": 4, "na18619": 4, "na18623": 4, "na18630": 4, "na18631": 4, "na18740": 4, "na18853": 4, "na18865": 4, "na18873": 4, "na18874": 4, "na18916": 4, "na18960": 4, "na18966": 4, "na18975": 4, "na18976": 4, "na18978": 4, "na18990": 4, "na19060": 4, "na19063": 4, "na19076": 4, "na19086": 4, "na19087": 4, "na19096": 4, "na19113": 4, "na19118": 4, "na19185": 4, "na19209": 4, "na19311": 4, "na19314": 4, "na19317": 4, "na19321": 4, "na19379": 4, "na19384": 4, "na19390": 4, "na19397": 4, "na19399": 4, "na19404": 4, "na19446": 4, "na19448": 4, "na19455": 4, "na19456": 4, "na19466": 4, "na19655": 4, "na19657": 4, "na19670": 4, "na19678": 4, "na19679": 4, "na19701": 4, "na19720": 4, "na19756": 4, "na19761": 4, "na19764": 4, "na19786": 4, "na20318": 4, "na20351": 4, "na20517": 4, "na20518": 4, "na20529": 4, "na20587": 4, "na20757": 4, "na20798": 4, "na20799": 4, "na20800": 4, "na20810": 4, "na20826": 4, "na20858": 4, "na20864": 4, "na20869": 4, "na20877": 4, "na20888": 4, "na20910": 4, "na21101": 4, "na21113": 4, "na21114": 4, "na21116": 4, "na21118": 4, "na21133": 4, "na21143": 4, "vcf_zarr_vers": 4, "last": [4, 28, 29, 66, 167, 168, 173], "easili": [4, 168], "form": [4, 171, 172, 174], "variant_contig_nam": 4, "later": [4, 6, 173], "ds2": [4, 23, 64, 169], "set_index": [4, 6, 169], "max_vari": [4, 19, 168, 169], "max_sampl": [4, 19, 168], "904165": 4, "909917": 4, "986963": 4, "1563691": 4, "1707740": 4, "152660491": 4, "153031688": 4, "153674876": 4, "153706320": 4, "154087368": 4, "row": [4, 6, 19, 26, 51, 56, 61, 62, 63, 168, 169], "too": [4, 45, 46, 47, 173], "df_variant": 4, "data_var": [4, 169], "startswith": 4, "variant_": 4, "to_datafram": [4, 168], "groupbi": [4, 168], "agg": 4, "lambda": [4, 61, 62, 63, 69, 168], "head": [4, 6, 168], "five": [4, 52], "referenc": [4, 168], "dtype": [4, 6, 15, 16, 17, 18, 25, 57, 61, 62, 63, 64, 168, 169, 173, 174], "possibli": [4, 61, 62, 63], "load": [4, 6, 37, 39, 40, 45, 46, 48, 53, 65, 111, 168, 170, 173, 174], "text": [4, 6, 39, 40, 48, 50], "csv": 4, "annot": 4, "regular": [4, 24, 66], "annotations_fil": 4, "1kg_annot": 4, "df": [4, 54, 168], "read_csv": [4, 6], "sep": 4, "index_col": [4, 6], "class": 4, "core": [4, 173, 174], "frame": [4, 168], "datafram": [4, 6, 24, 51, 54, 168], "3500": 4, "entri": [4, 21], "na21144": 4, "total": [4, 25, 67, 109, 163], "null": [4, 24], "popul": [4, 6, 10, 25, 58, 61, 62, 63, 69, 132, 168, 170, 172, 173], "superpopul": 4, "isfemal": 4, "purplehair": 4, "caffeineconsumpt": 4, "int64": [4, 164, 166, 167, 168, 169, 173], "116": [4, 6, 173], "kb": 4, "gbr": 4, "eur": 4, "hg00097": 4, "hg00098": 4, "hg00100": 4, "na21137": 4, "gih": 4, "sa": 4, "na21141": 4, "na21142": 4, "join": [4, 6, 168, 173], "ds_annot": 4, "to_xarrai": 4, "renam": [4, 6, 173], "left": [4, 6, 48], "reset_index": 4, "reset_coord": 4, "2kb": [4, 66, 168, 169, 173], "x27": [4, 6], "284b": 4, "284variant": 4, "10879allel": 4, "fin": 4, "ch": 4, "pur": 4, "cdx": 4, "clm": 4, "ib": [4, 30, 129], "pel": 4, "khv": 4, "acb": 4, "gwd": 4, "pjl": 4, "esn": 4, "beb": 4, "msl": 4, "stu": 4, "itu": 4, "ceu": 4, "yri": 4, "chb": 4, "jpt": 4, "lwk": 4, "mxl": 4, "asw": 4, "tsi": 4, "ea": 4, "amr": 4, "afr": 4, "boolfals": 4, "truearrai": 4, "int644": 4, "5arrai": 4, "relev": [4, 6, 172], "seri": 4, "built": 4, "usual": [4, 6, 173], "enough": [4, 168], "ok": 4, "distribut": [4, 6, 24, 168, 170, 173, 174], "contin": 4, "to_seri": [4, 168], "value_count": 4, "1018": 4, "661": 4, "617": 4, "535": 4, "describ": [4, 6, 10, 24, 25, 27, 55, 59, 66, 168, 171, 172, 173, 174], "000000": [4, 168], "983714": 4, "std": [4, 168], "702349": 4, "min": [4, 10, 168], "max": [4, 168], "fewer": [4, 45, 46, 47, 61, 62, 63, 168, 174], "len": 4, "76": [4, 27], "72": 4, "55": [4, 63, 166, 168], "34": [4, 56, 168, 173], "415493": 4, "580549": 4, "hoc": [4, 168], "uncov": 4, "biolog": [4, 70], "insight": [4, 52], "base": [4, 6, 10, 25, 32, 33, 34, 38, 52, 54, 60, 61, 66, 97, 133, 134, 137, 166, 168, 170, 172, 173, 174], "appli": [4, 6, 25, 48, 61, 62, 63, 64, 69, 70, 168, 173], "tupl": [4, 37, 39, 40, 58, 66], "2418": 4, "2367": 4, "1929": 4, "1864": 4, "494": 4, "466": 4, "451": 4, "150": 4, "111": [4, 6, 146], "often": [4, 6, 168, 173], "plot": [4, 6, 168], "feel": 4, "attr": 4, "long_nam": 4, "hist": [4, 168], "rang": [4, 25, 58, 165, 170, 174], "30": [4, 56, 168, 173], "bin": [4, 168], "edgecolor": 4, "qc": 4, "process": [4, 6, 45, 46, 47, 48, 49, 54, 119, 145, 169, 170, 173, 174], "poor": 4, "iter": 4, "collect": 4, "metric": [4, 56], "equival": [4, 29, 44, 108, 110, 145, 169], "sample_qc": 4, "begin": [4, 6], "sample_": 4, "sample_n_cal": [4, 103, 169], "sample_call_r": [4, 100, 169], "sample_n_het": [4, 104, 169], "sample_n_hom_ref": [4, 106, 169], "sample_n_hom_alt": [4, 105, 169], "sample_n_non_ref": [4, 107, 169], "int64dask": 4, "rate": [4, 168], "sample_gq_mean": 4, "dim": [4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 52, 55, 58, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 168, 173], "60": [4, 6, 19, 168], "sample_dp_mean": 4, "recent": [4, 59, 172, 173], "issu": [4, 40, 170, 172, 173], "934": 4, "scatter": [4, 6], "outlier": 4, "cutoff": 4, "sel": [4, 58, 168, 169], "print": [4, 169, 173], "remain": 4, "250": [4, 25, 168], "complic": 4, "ab": 4, "fraction": [4, 67, 100, 144, 163], "nan": [4, 6, 7, 25, 28, 29, 30, 31, 35, 55, 56, 63, 74, 130, 168, 174], "ad1": 4, "dict": [4, 6, 20, 36, 39, 43, 44, 45, 46, 47, 49, 53, 64, 65, 68, 70], "pipe": [4, 168], "adsum": 4, "Then": [4, 6, 46, 173], "condit": [4, 168], "heterozygot": 4, "balanc": 4, "hom_ref": 4, "het": 4, "hom_alt": 4, "filter_condition_ab": 4, "filter_mask": 4, "fraction_filt": 4, "2f": 4, "65": [4, 63, 168], "compar": [4, 6, 169], "time": [4, 6, 37, 39, 40, 46, 47, 173, 174], "won": [4, 174], "26mb": 4, "variant_n_cal": [4, 152, 168, 169], "variant_call_r": [4, 144, 168, 169], "variant_n_het": [4, 153, 168, 169], "variant_n_hom_ref": [4, 155, 168, 169], "variant_n_hom_alt": [4, 154, 168, 169], "variant_n_non_ref": [4, 156, 168, 169], "250b": 4, "1kb": [4, 169], "2sampl": 4, "250ploidi": 4, "variant_allele_count": [4, 9, 17, 140, 163, 168, 173], "uint64dask": 4, "With": [4, 71, 72, 88, 140, 168, 172, 173], "uint64": [4, 16, 17, 18, 168, 169, 173], "variant_allele_tot": [4, 143, 168], "variant_allele_frequ": [4, 141, 168], "restrict": [4, 173], "hardi": [4, 25, 27], "weinberg": [4, 25, 27], "equilibrium": [4, 25, 27], "tell": 4, "u": [4, 6, 71, 74, 87, 90, 94, 102, 120, 140, 145, 146, 148, 172, 173], "being": [4, 168, 173, 174], "regener": 4, "safe": 4, "u3": [4, 168, 169], "36b": [4, 169], "41": [4, 168, 173], "variant_hwe_p_valu": [4, 27, 147, 169], "variant_genotype_count": [4, 18, 27, 146, 169], "261kb": 4, "genotype_id": [4, 18, 169], "10879genotyp": 4, "3allel": 4, "p": [4, 6, 24, 25, 26, 27, 59, 66, 147, 150, 174], "hwe": [4, 27, 147], "observ": [4, 31, 48, 55, 85, 131, 146], "sort": [4, 54, 57, 63, 146], "triallel": [4, 146], "triploid": [4, 146], "000": [4, 45, 46, 47, 146], "001": [4, 146], "011": [4, 146], "002": [4, 146], "012": [4, 146], "112": [4, 29, 146], "022": [4, 146], "122": [4, 146], "222": [4, 146, 173], "254": 4, "234": 4, "u3dask": 4, "given": [4, 6, 18, 31, 56, 168, 173, 174], "outlin": [4, 54, 63, 174], "genotypespandasindexpandasindex": 4, "1e": [4, 24, 169], "final": [4, 6, 28, 29, 38, 45, 46, 47, 65, 169, 174], "8394": 4, "linear": [4, 6, 26], "regress": [4, 25, 26, 66, 97], "trait": [4, 24, 26, 66, 139, 149, 150, 151], "ds_lr": 4, "gwas_linear_regress": 4, "add_intercept": [4, 26, 66], "covari": [4, 24, 26, 66, 89, 108], "37mb": 4, "45": [4, 25, 28, 29, 168, 173], "variant_linreg_beta": [4, 26, 149], "67kb": 4, "5439": 4, "variant_linreg_t_valu": [4, 26, 151], "variant_linreg_p_valu": [4, 26, 150], "201kb": 4, "17mb": 4, "8394trait": 4, "1genotyp": 4, "beta": [4, 6, 10, 24, 26, 122, 149, 151], "196": 4, "127": [4, 59], "48": [4, 59, 168, 173, 174], "131": [4, 61, 62, 63, 69], "32": [4, 13, 56, 69, 168, 173, 174], "37": [4, 168, 173], "doesn": [4, 173, 174], "manhattan": 4, "qq": 4, "seaborn": 4, "sn": 4, "matplotlib": [4, 6], "inlin": [4, 38], "manhattan_plot": 4, "variant_linreg_log_p_valu": 4, "log10": 4, "astyp": [4, 6, 168, 174], "overflow": 4, "cumulative_po": 4, "mojon": 4, "video_notebook": 4, "blob": 4, "master": 4, "20plot": 4, "20in": 4, "20python": 4, "ipynb": 4, "cell": [4, 173], "running_po": 4, "group_df": 4, "append": [4, 44], "concat": [4, 6], "color": [4, 173], "els": [4, 52], "relplot": 4, "hue": 4, "palett": 4, "blue": [4, 6], "orang": 4, "linewidth": 4, "legend": 4, "none": [4, 7, 8, 20, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 58, 63, 65, 66, 68, 69, 70, 89, 90, 91, 92, 93, 139, 149, 151, 166, 167, 168, 174], "aspect": [4, 174], "ax": [4, 60, 108, 111, 112, 168], "set_xlabel": 4, "chromosom": [4, 39, 40, 70, 119, 168], "set_xtick": 4, "median": 4, "set_xticklabel": 4, "math": 4, "pyplot": [4, 6], "plt": [4, 6], "qq_plot": 4, "squeez": 4, "expected_p": 4, "arang": [4, 69], "observed_p": 4, "max_val": 4, "ceil": 4, "fig": 4, "subplot": 4, "figsiz": [4, 6, 168], "scatterplot": 4, "x_pred": 4, "linspac": 4, "lineplot": 4, "xlim": 4, "ylim": 4, "explain": [4, 109, 110, 168, 173], "ancestri": 4, "just": [4, 168, 173, 174], "better": [4, 38, 174], "princip": [4, 59, 108, 109, 110, 111, 112], "pca": [4, 111], "ds_pca": 4, "stat": [4, 66, 170, 173], "count_call_alternate_allel": 4, "Or": 4, "zero": [4, 6, 10, 25, 48, 51, 52, 61, 62, 63, 69, 173], "variant_mask": 4, "call_alternate_allele_count": 4, "sample_pca_project": [4, 59, 112], "453594": 4, "128805": 4, "008168": 4, "8012085": 4, "537296": 4, "0794808": 4, "496218": 4, "31961": 4, "116499": 4, "6827672": 4, "6817017": 4, "957277": 4, "873404": 4, "404314": 4, "85919": 4, "382873": 4, "368455": 4, "384331": 4, "974406": 4, "576627": 4, "124643": 4, "4210625": 4, "5393088": 4, "0124567": 4, "754401": 4, "414771": 4, "358787": 4, "7951679": 4, "4263666": 4, "985675": 4, "062882": 4, "688103": 4, "351276": 4, "205051": 4, "7339797": 4, "17502": 4, "3491": 4, "10kb": [4, 168, 169, 173], "sample_pca_compon": [4, 108], "140kb": 4, "sample_pca_explained_vari": [4, 110], "40b": [4, 168], "sample_pca_explained_variance_ratio": [4, 109], "sample_pca_load": [4, 111], "int16": 4, "2mb": 4, "250compon": 4, "10variant": 4, "3491genotyp": 4, "52": [4, 25, 168, 173], "136": 4, "int16dask": 4, "27": [4, 63, 168, 173], "81": 4, "two": [4, 6, 7, 8, 9, 12, 16, 21, 22, 31, 46, 55, 56, 58, 61, 62, 63, 69, 119, 168, 173, 174], "notic": 4, "cluster": [4, 174], "sample_pca_projection_0": 4, "sample_pca_projection_1": 4, "sample_pca_projection_2": 4, "rerun": 4, "sex": [4, 40, 41], "copi": [4, 61, 63, 70, 119, 120, 168, 173], "back": 4, "caffein": 4, "consumpt": 4, "locu": [4, 6, 18, 30, 59, 166], "clearli": 4, "appar": [4, 6], "varieti": [6, 170], "approach": [6, 28, 29], "structur": [6, 10, 20, 28, 29, 57, 60, 61, 62, 63, 64, 69, 133, 134, 135, 136, 137, 138, 170, 173], "addit": [6, 39, 43, 44, 45, 46, 47, 53, 57, 61, 62, 63, 68, 69, 70, 173, 174], "between": [6, 7, 10, 21, 25, 30, 54, 56, 58, 59, 69, 111, 114, 123, 166, 167, 168, 173, 174], "cleveland": 6, "et": [6, 7, 8, 24, 25, 26, 27, 28, 29, 59, 63, 69], "al": [6, 7, 8, 24, 25, 26, 27, 28, 29, 59, 63, 69], "2012": [6, 25, 69], "6473": 6, "3534": 6, "individu": [6, 10, 25, 26, 30, 31, 55, 59, 61, 62, 63, 66, 69, 120, 168], "across": [6, 33, 34, 66, 113, 157, 168, 173, 174], "52843": 6, "loci": [6, 69], "cleveland2012_pedigre": 6, "gz": [6, 48, 174], "cleveland2012_snps1000": 6, "inspect": 6, "commonli": [6, 40, 41, 59, 112, 173], "rcparam": 6, "figur": 6, "simpl": [6, 168, 173], "tabular": [6, 19, 168], "three": [6, 7, 8, 9, 21, 22, 27, 45, 46, 47, 55, 58, 64, 65, 168, 173], "column": [6, 19, 26, 27, 61, 62, 63, 89, 139, 168, 169], "patern": 6, "matern": 6, "while": [6, 168, 173, 174], "ped": 6, "quit": 6, "reason": [6, 173], "recommend": [6, 48, 173, 174], "sire": 6, "dam": 6, "appear": 6, "ascend": [6, 28, 54], "safer": 6, "treat": [6, 45, 46, 47, 63, 67, 163, 174], "mistaken": 6, "especi": 6, "parent_id": [6, 57, 60, 61, 62, 63, 64, 69, 94], "dataarrai": [6, 7, 8, 9, 12, 16, 21, 22, 55, 58, 168, 169, 173], "104kb": 6, "4279": 6, "6465": 6, "6466": 6, "1129": 6, "5129": 6, "6472": 6, "52kb": 6, "6471": 6, "16b": [6, 164, 168], "dataarraysampl": 6, "6473parent": 6, "samplespandasindexpandasindex": 6, "6464": 6, "6467": 6, "6468": 6, "6469": 6, "6470": 6, "parentspandasindexpandasindex": 6, "translat": 6, "likewis": 6, "primarili": [6, 70], "differenti": 6, "mani": [6, 23, 168, 172, 174], "ident": [6, 30, 31, 52, 69, 168], "207kb": 6, "2coordin": 6, "combin": [6, 18, 28, 29, 43], "typic": [6, 38, 43, 54, 168, 174], "except": [6, 21, 41, 45, 46, 47, 167, 168, 169, 174], "normal": [6, 66, 173], "re": [6, 35, 66, 173], "invalid": [6, 57, 64], "parent_indic": [6, 20, 60, 61, 62, 63, 64, 69], "4278": 6, "1128": 6, "5128": 6, "neg": [6, 24, 56, 95, 101, 166], "unkno": 6, "6463": 6, "3674": 6, "6471arrai": 6, "serv": [6, 44], "robust": 6, "record": [6, 45, 46, 47, 61, 62, 63, 173], "preserv": [6, 65, 174], "subset": [6, 28, 29, 35, 36, 61, 64, 130, 168, 170], "reorder": 6, "fast": 6, "numer": [6, 69, 120], "howev": [6, 49, 61, 69, 163, 168, 173, 174], "among": [6, 25, 28, 29, 30, 55, 63, 122, 129, 137], "simplifi": [6, 168], "assumpt": [6, 66, 170, 174], "unrel": [6, 10, 61, 62, 63], "anoth": [6, 29, 168, 173], "even": [6, 38, 60, 120, 174], "hold": [6, 8, 10, 11, 12, 13, 15, 16, 17, 18, 20, 23, 25, 26, 30, 31, 32, 33, 34, 55, 57, 59, 60, 61, 62, 63, 64, 67, 69, 163], "inaccur": 6, "varianc": [6, 24, 109, 110], "caus": [6, 35, 173], "mendelian": [6, 69], "arm": [6, 62, 63], "predigree_kinship": 6, "allow_half_found": [6, 61, 62, 63], "return_relationship": [6, 62, 63], "stat_pedigree_kinship": [6, 63, 137], "stat_pedigree_relationship": [6, 29, 35, 63, 138], "samples_0": [6, 10, 25, 28, 29, 30, 35, 59, 60, 62, 63, 64, 96, 122, 125, 126, 127, 128, 129, 130, 133, 135, 136, 137, 138], "samples_1": [6, 10, 25, 28, 29, 30, 35, 59, 60, 62, 63, 64, 96, 122, 125, 126, 127, 128, 129, 130, 133, 135, 136, 137, 138], "335mb": 6, "mul": 6, "chunktyp": [6, 168, 173], "deriv": [6, 25, 61, 63, 119, 138, 168], "6473samples_1": 6, "6473dask": 6, "319": 6, "67": [6, 168], "twice": 6, "unfortun": 6, "propag": [6, 61, 62, 63], "assign_coord": [6, 18, 58, 64, 168], "lazi": [6, 168], "think": [6, 172], "promis": 6, "immedi": 6, "evalu": [6, 28, 29, 38, 66, 168], "015625": 6, "01111412": 6, "01885986": 6, "01507568": 6, "5324707": 6, "0324707": 6, "64731": 6, "008972": 6, "02167": 6, "01508": 6, "5325": 6, "032arrai": 6, "samples_0pandasindexpandasindex": 6, "samples_1pandasindexpandasindex": 6, "matshow": 6, "attempt": [6, 170], "realiz": [6, 25], "upon": [6, 25], "share": 6, "marker": [6, 25], "construct": [6, 44, 159], "datatyp": 6, "bgen": [6, 14, 168, 172], "991": 6, "992": 6, "994": 6, "996": [6, 168], "997": [6, 168], "998": [6, 168], "999": [6, 168], "1000": [6, 36, 38, 45, 46, 47, 66, 168, 170], "584": 6, "585": 6, "587": 6, "588": 6, "589": 6, "transpos": 6, "8kb": [6, 168], "28kb": 6, "dataarrayvari": 6, "1000sampl": 6, "35341": 6, "0arrai": 6, "variantspandasindexpandasindex": 6, "590": 6, "591": 6, "592": 6, "593": 6, "594": 6, "gen": 6, "0xarrai": 6, "3534variant": 6, "1000coordin": 6, "float641": 6, "2008": [6, 25], "term": [6, 26], "m": [6, 25, 26, 28, 29, 56, 108, 110, 173], "nucleotid": [6, 168], "respect": [6, 27, 170], "purpos": [6, 48, 168, 170], "unselect": 6, "occur": [6, 38, 63, 168], "select": [6, 25, 28, 29, 51, 52, 54, 59, 64, 159, 168, 169, 172], "inbreed": [6, 61, 63, 134], "necessarili": 6, "natur": [6, 26, 174], "randomli": [6, 30, 119], "breed": [6, 25], "program": 6, "sensit": 6, "rare": 6, "initi": [6, 23, 63, 69], "naiv": [6, 168], "achiev": [6, 174], "divid": [6, 7, 8, 9, 12, 16, 21, 22, 25, 44, 52, 55, 58, 174], "sample_frequ": [6, 25], "stat_genomic_relationship": [6, 25, 29, 126], "stat_vanraden_grm_na": 6, "clariti": 6, "ancestral_frequ": [6, 25], "perfect": 6, "task": [6, 46, 47, 168, 173, 174], "long": [6, 61, 62, 63, 173, 174], "tril_idx": 6, "tril_indic": 6, "alpha": [6, 66, 97], "xlabel": 6, "ylabel": [6, 168], "tmp": [6, 174], "ipykernel_2784": 6, "892134664": 6, "futurewarn": 6, "map": [6, 36, 56, 63, 168], "whose": [6, 45, 46, 47, 65, 168], "pair": [6, 7, 10, 20, 21, 25, 30, 51, 52, 56, 59, 63, 114, 123, 133, 166, 168], "cross": 6, "progeni": [6, 69], "give": [6, 168], "wasn": 6, "alreadi": [6, 17, 26, 37, 51, 52, 61], "present": [6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 48, 50, 51, 52, 55, 58, 60, 61, 62, 63, 64, 67, 69, 163, 168, 174], "fact": 6, "bia": 6, "increas": [6, 26, 46, 47, 61, 62, 63, 119, 165, 166, 174], "obtain": [6, 174], "surrog": 6, "mcpeek": 6, "2004": 6, "unbias": 6, "Their": 6, "invers": [6, 28, 29, 35, 61, 62, 63, 69, 127, 130, 135, 136], "weight": 6, "reflect": [6, 10], "equat": 6, "hat": [6, 10, 61], "textit": 6, "interc": 6, "phi": [6, 61], "vector": [6, 56, 108], "ones": 6, "although": 6, "straightforward": [6, 174], "sub": [6, 35, 63], "invert": [6, 35], "stat_inverse_pedigree_kinship": 6, "stat_inverse_relationship": [6, 28, 35, 130], "blue_weight": 6, "blue_frequ": 6, "And": 6, "stat_vanraden_grm_blu": 6, "3477141311": 6, "2017": [6, 10, 61, 62, 63, 69], "coeffici": [6, 59, 61, 63, 96, 134], "probabl": [6, 14, 30, 31, 36, 37, 38, 59, 61, 62, 63, 83, 119, 129, 168], "approxim": [6, 25, 38, 174], "ibd": [6, 59, 61, 62, 63, 119], "descent": 6, "averag": [6, 10], "rel": [6, 10, 64], "bias": 6, "underestim": 6, "prior": 6, "knowledg": 6, "frac": [6, 10, 61], "_0": [6, 10], "rank": 6, "multi": 6, "therefor": [6, 31, 48, 61, 62, 63, 168, 174], "call_allele_frequ": [6, 30, 72], "per": [6, 7, 9, 11, 15, 16, 17, 21, 22, 31, 45, 46, 47, 55, 58, 65, 69, 173], "multipli": 6, "un": [6, 60], "stat_weir_goudet_grm": 6, "stat_weir_goudet_beta": [6, 10, 122], "uncorrect": 6, "70656024": 6, "plant": [6, 25], "anim": 6, "studi": 6, "budget": 6, "limit": [6, 27, 39, 42, 45, 50, 168, 173], "constraint": 6, "deceas": 6, "avail": [6, 7, 9, 21, 22, 38, 58, 168, 173, 174], "choos": [6, 174], "smaller": [6, 36, 45, 46, 66, 168, 169, 170, 174], "h": [6, 25, 28, 29, 127, 128], "accuraci": [6, 25], "complet": [6, 23, 76, 173, 174], "bmatrix": 6, "nan_": 6, "pad": [6, 45, 46, 47], "messier": 6, "notat": [6, 48], "gap": 6, "imag": [6, 173], "sake": 6, "genomic_sampl": [6, 28, 29], "isin": [6, 169], "earlier": 6, "a_": 6, "goal": [6, 168], "h_": 6, "factor": [6, 28, 29], "tau": [6, 28, 29, 61, 62, 63, 69], "omega": [6, 28, 29], "martini": [6, 28, 29], "2018": [6, 28, 29, 63], "fine": [6, 174], "tune": 6, "influenc": 6, "beyond": 6, "scope": 6, "along": [6, 7, 9, 21, 22, 26, 40, 48, 58, 64, 89, 139, 161, 162, 166, 168], "axi": [6, 60, 89, 139, 168], "uneven": [6, 35], "dure": [6, 168, 173, 174], "stat_vanraden_hrm_blu": 6, "pedigree_relationship": [6, 28, 29], "stat_hybrid_relationship": [6, 29, 128], "verifi": 6, "assert_array_almost_equ": 6, "loc": 6, "hickei": 6, "j": [6, 21, 25, 26, 27, 28, 29, 51, 54, 56, 59, 61, 62, 63, 66, 69, 166, 173], "forni": 6, "livestock": 6, "g3": [6, 25], "429": 6, "435": 6, "doi": 6, "1534": 6, "2fg3": 6, "001453": 6, "schrauf": [6, 28, 29], "garcia": [6, 28, 29], "baccino": [6, 28, 29], "pimentel": [6, 28, 29], "munilla": [6, 28, 29], "rogberg": 6, "mu\u00f1oz": [6, 28, 29], "cantet": [6, 28, 29], "reimer": [6, 28, 29], "gao": [6, 28, 29], "wimmer": [6, 28, 29], "simian": [6, 28, 29], "procedur": [6, 28, 29], "evolut": [6, 28, 29], "1186": 6, "s12711": 6, "018": 6, "0386": 6, "wu": 6, "ober": 6, "complex": [6, 24, 170], "biometr": 6, "359": 6, "367": 6, "1111": 6, "0006": 6, "341x": 6, "00180": 6, "predict": [6, 25, 26, 66, 97, 98, 99], "journal": [6, 25, 27, 28, 29, 59], "dairi": [6, 25, 28, 29], "scienc": [6, 25, 26, 28, 29, 172], "91": [6, 25], "4414": [6, 25], "4423": [6, 25], "3168": 6, "jd": 6, "2007": 6, "0980": 6, "unifi": [6, 10, 28, 29], "character": [6, 10], "206": [6, 10], "2085": [6, 10], "2103": [6, 10], "198424": 6, "stat_diverg": [7, 21, 123], "window_by_posit": [7, 8, 9, 21, 22, 51, 52, 55, 58, 168], "window_by_vari": [7, 8, 9, 21, 22, 51, 52, 55, 58, 168], "str": [7, 8, 20, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 58, 65, 66, 68, 168], "formula": [7, 10, 61], "hudson": 7, "1992": 7, "elabor": 7, "bhatia": 7, "2013": 7, "nei": 7, "1986": [7, 69], "tskit": 7, "hashabl": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 69, 163, 165, 166, 167], "diverg": [7, 123], "stat_divergence_spec": [7, 21], "otherwis": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 41, 48, 50, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167], "behavior": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55, 57, 58, 59, 66, 67, 69, 163, 164, 165, 166, 167, 168], "stat_fst_spec": [7, 58], "n_variant": [7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 52, 55, 57, 58, 61, 62, 63, 66, 69, 70, 164, 166, 167, 168, 169, 173], "n_sampl": [7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 46, 47, 52, 55, 57, 58, 61, 62, 63, 66, 69, 70, 164, 166, 167, 168, 169, 173], "sample_cohort": [7, 8, 9, 12, 16, 21, 22, 55, 58, 101, 168], "stat_fst": [7, 58, 114, 168], "16666667": 7, "33333333": [7, 8, 25, 61, 62], "22222222": 7, "h1": [8, 117, 118], "h12": [8, 116], "h123": [8, 115], "h2": [8, 118], "detect": [8, 24], "signatur": 8, "soft": 8, "sweep": 8, "garud": [8, 115, 116, 117, 118], "2015": [8, 26], "call_genotype_spec": [8, 13, 14, 15, 17, 18, 23, 26, 32, 33, 34, 40, 59, 65, 67, 69, 70, 163, 173], "sample_cohort_spec": [8, 16, 55], "sequenc": [8, 25, 26, 43, 44, 45, 46, 47, 49, 58, 66], "union": [8, 20, 24, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 56, 58, 64, 65, 66, 68, 69], "stat_garud_h1": [8, 117], "stat_garud_h1_spec": 8, "stat_garud_h12": [8, 116], "stat_garud_h12_spec": 8, "stat_garud_h123": [8, 115], "stat_garud_h123_spec": 8, "stat_garud_h2_h1": [8, 118], "stat_garud_h2_h1_spec": 8, "notimplementederror": [8, 27, 60, 69], "valueerror": [8, 13, 18, 25, 27, 28, 29, 40, 41, 44, 51, 52, 54, 57, 59, 60, 61, 62, 63, 66, 67, 69, 163, 166, 173], "375": [8, 21, 60, 63], "625": [8, 21, 28, 29, 35, 60, 63], "stat_divers": [9, 22, 124, 168], "tajima": [9, 121, 124], "variant_allele_count_spec": [9, 17, 163], "divers": [9, 21, 124, 168], "stat_diversity_spec": [9, 22], "stat_tajimas_d_spec": 9, "stat_tajimas_d": [9, 121], "88883234": 9, "18459998": 9, "40517586": 9, "10393559": 9, "stat_identity_by_st": [10, 30, 129], "weir": [10, 59, 63, 122], "goudet": [10, 63, 122], "diagon": [10, 24, 51, 61, 63, 125, 133, 137], "self": [10, 59, 61, 63, 125, 137], "accur": 10, "stat_identity_by_state_spec": [10, 30], "stat_weir_goudet_beta_spec": 10, "n_allel": [10, 13, 69, 70], "seed": [10, 11, 13, 15, 17, 18, 23, 25, 30, 31, 57, 61, 62, 63, 66, 69, 70, 168, 173], "inherit": [10, 69, 119, 120, 174], "s0": [10, 11, 12, 13, 15, 16, 17, 18, 23, 30, 31, 57, 60, 61, 62, 63, 64, 69, 168, 169, 173], "s1": [10, 11, 12, 13, 15, 16, 17, 18, 23, 30, 31, 57, 60, 61, 62, 63, 64, 69, 168, 169, 173], "s2": [10, 12, 16, 30, 57, 60, 61, 62, 63, 64, 69, 168, 169, 173], "beta0": 10, "beta_correct": 10, "bruce": [10, 59, 63, 69], "j\u00e9r\u00f4me": [10, 63], "related": [10, 25, 59], "call_allele_count": [11, 15, 16, 17, 25, 31, 71, 173], "frequenc": [11, 12, 25, 30, 51, 52, 59, 72, 88, 141, 163, 168], "call_allele_count_spec": [11, 15, 16, 17, 31, 173], "count_call_allel": [11, 16, 17, 25, 31, 173], "call_allele_frequency_spec": [11, 30], "cohort_allele_count": [12, 16, 21, 22, 87], "cohort_allele_count_spec": [12, 16, 21, 22], "count_cohort_allel": [12, 21, 22], "cohort_allele_frequency_spec": 12, "s3": [12, 16, 60, 61, 62, 63, 64, 69, 168, 169, 173, 174], "call_genotype_index_spec": [13, 173], "call_genotype_index_mask_spec": 13, "missing_pct": [13, 23, 25, 70, 168, 169, 173], "call_genotype_index": [13, 79, 173], "call_genotype_prob": [14, 83], "threshold": [14, 51, 52], "hard": 14, "read_bgen": [14, 36, 38, 173], "call_genotype_probability_spec": [14, 37], "met": 14, "exceed": 14, "mask": [14, 36, 38, 59, 168], "call_genotype_mask_spec": [14, 40, 59, 65, 69, 70], "uint8": [15, 25, 36, 38, 173], "argument": [17, 23, 29, 53, 56, 68, 168, 173, 174], "liter": [17, 25, 28, 29, 30, 56, 60, 61, 62, 63, 69], "multiset": 18, "cardin": 18, "manner": 19, "denot": [19, 56], "separ": [19, 46, 66, 139, 168, 173, 174], "genotype_phas": 19, "unphas": [19, 70, 81], "maximum": [19, 41, 45, 46, 47, 59, 64, 173, 174], "tabl": 19, "truncat": [19, 45, 46, 47], "genotypedisplai": 19, "printabl": 19, "graph_attr": 20, "node_attr": [20, 173], "edge_attr": 20, "direct": [20, 63], "acycl": 20, "parent_spec": [20, 57, 60, 61, 62, 63, 64, 69, 119, 120], "through": [20, 26, 37, 39, 40, 49, 66, 168, 170], "node": [20, 173], "broadcast": 20, "edg": 20, "runtimeerror": 20, "instal": [20, 170], "digraph": 20, "66666667": [21, 22, 25, 62], "83333333": [21, 22], "partial": [23, 25, 67, 76, 163], "call_genotype_complete_spec": 23, "call_genotype_complete_mask_spec": 23, "call_genotype_complet": [23, 76], "call_genotype_complete_mask": [23, 75], "overwrit": [23, 173], "explicitli": [23, 27, 168], "futher": 23, "ld": [24, 51, 52, 54, 93, 159], "reg_covar": 24, "cheng": 24, "2020": [24, 25, 48, 66, 172], "ol": [24, 26], "2d": [24, 26, 66, 89, 139], "gaussianmixtur": 24, "unlik": [24, 168], "alwai": [24, 51, 52, 133, 168], "second": [24, 26, 30, 46, 64, 84, 89, 139, 168, 174], "mixtur": [24, 67, 163, 168], "largest": 24, "compos": 24, "test_q": 24, "q_var": 24, "pval": 24, "ramachandran": 24, "l": [24, 25, 28, 29, 66, 69], "crawford": 24, "enabl": [24, 173, 174], "enrich": 24, "underli": [24, 168, 174], "plo": 24, "e1008855": 24, "lab": 24, "aka": [25, 28, 29], "grm": [25, 126], "autopolyploid": [25, 61, 62, 63, 67, 69, 163], "ashraf": 25, "2016": [25, 59], "bilton": 25, "shrinkag": 25, "jannick": 25, "aim": 25, "densiti": [25, 51, 52], "ancestr": 25, "under": [25, 169], "infer": [25, 26, 32, 33, 34], "stat_genomic_relationship_spec": [25, 29], "cannot": [25, 26, 37, 39, 40, 41, 42, 173], "incorrect": 25, "depend": [25, 26, 38, 173, 174], "monomorph": 25, "rrblup": 25, "93617021": 25, "21276596": 25, "72340426": 25, "17021277": 25, "04255319": 25, "68085106": 25, "9744836": 25, "16978417": 25, "58417266": 25, "33778858": 25, "45323741": 25, "47619048": 25, "89496403": 25, "62446043": 25, "34820144": 25, "79951397": 25, "imput": [25, 74], "call_dosage_imput": 25, "14337789": 25, "49331713": 25, "2272175": 25, "32806804": 25, "75577157": 25, "527339": 25, "29404617": 25, "byrn": 25, "f\u00e9": 25, "czaban": 25, "asp": 25, "pedersen": 25, "lenk": 25, "roulund": 25, "didion": 25, "jensen": 25, "janss": 25, "herit": [25, 66], "famili": [25, 40, 41, 59], "pool": 25, "perenni": 25, "ryegrass": 25, "theoret": [25, 61, 62, 63, 69], "129": 25, "develop": [25, 170, 172, 173], "phd": 25, "thesi": 25, "univers": 25, "otago": 25, "1405": 25, "1413": 25, "ridg": [25, 66, 97], "kernel": 25, "255": 25, "continu": [26, 66, 139], "solv": 26, "simultan": 26, "facilit": [26, 168], "orthogon": [26, 66], "phenotyp": [26, 28, 29, 40, 41, 139], "consequ": 26, "rotat": [26, 173], "signific": 26, "independ": [26, 52, 54], "1d": [26, 66, 139], "covariates_spec": [26, 66], "traits_spec": [26, 66], "intercept": [26, 66], "valid": [26, 173], "parameter": 26, "free": [26, 59, 168], "block": [26, 37, 39, 40, 66, 97, 98], "tall": 26, "skinni": 26, "num": [26, 27, 59, 66], "hasti": 26, "trevor": 26, "robert": 26, "tibshirani": 26, "jerom": 26, "friedman": 26, "2009": [26, 28, 29], "element": [26, 36, 38, 130, 133], "mine": 26, "springer": 26, "busi": 26, "media": 26, "loh": 26, "ru": 26, "georg": 26, "tucker": 26, "brendan": 26, "k": 26, "bulik": 26, "sullivan": 26, "bjarni": 26, "vilhj\u00e1lmsson": 26, "hilari": 26, "finucan": 26, "rani": 26, "salem": 26, "daniel": 26, "chasman": 26, "bayesian": 26, "model": [26, 59, 66, 168, 172], "power": [26, 168], "exact": 27, "wigginton": 27, "2005": 27, "precomput": 27, "keyerror": [27, 57], "jani": 27, "david": 27, "cutler": 27, "goncalo": 27, "abecasi": 27, "american": [27, 59], "human": [27, 59], "887": 27, "genomic_inverse_relationship": 28, "pedigree_inverse_relationship": 28, "pedigree_subset_inverse_relationship": [28, 29], "hybrid": [28, 29, 127, 128], "hrm": [28, 29], "stat_inverse_relationship_spec": [28, 29, 35], "stat_pedigree_inverse_relationship_spec": [28, 29, 62], "boolean": [28, 29, 35, 64, 168], "absent": [28, 29, 66, 98], "expand": [28, 29], "legarra": [28, 29], "aguil": [28, 29], "2010": [28, 29], "stat_hybrid_inverse_relationship_spec": 28, "125": [28, 29, 35, 63], "subset_sampl": [28, 35], "stat_hybrid_inverse_relationship": [28, 127], "round": [28, 29, 35, 48], "987": 28, "332": 28, "549": 28, "574": 28, "247": 28, "roberg": [28, 29], "aguilar": [28, 29], "misztal": [28, 29], "4656": [28, 29], "4663": [28, 29], "johnson": [28, 29], "tsuruta": [28, 29], "lawlor": [28, 29], "holstein": [28, 29], "743": [28, 29], "752": [28, 29], "stat_pedigree_relationship_spec": [29, 63], "stat_hybrid_relationship_spec": 29, "adjac": 29, "084": 29, "056": 29, "028": 29, "653": 29, "013": 29, "281": [29, 173], "576": 29, "drawn": [30, 31], "random": [30, 31, 59, 66, 69, 70], "multipl": [30, 37, 39, 40, 43, 45, 46, 47, 49, 61, 62, 63, 69, 166, 170, 173], "heterozygos": [31, 55, 67, 85, 131, 163], "polyploid": [31, 170], "haploid": 31, "call_heterozygosity_spec": [31, 55], "call_heterozygos": [31, 55, 85], "call_genotype_fil": [32, 77], "call_genotype_fill_spec": [32, 69], "call_ploidy_spec": [32, 33, 34], "call_ploidi": [33, 34, 86], "infer_call_ploidi": [33, 34], "sample_ploidy_spec": 33, "variant_ploidy_spec": 34, "subset_rechunk": 35, "567": 35, "233": 35, "region": [36, 44, 45, 46, 47, 48, 49, 174], "chunk_width": [36, 38, 45, 46, 47, 174], "compressor": [36, 38, 45, 46, 47, 48, 174], "blosc": [36, 38, 45, 46, 47], "cname": [36, 38, 45, 46, 47], "zstd": [36, 38, 45, 46, 47], "clevel": [36, 38, 45, 46, 47], "shuffl": [36, 38, 45, 46, 47], "bitshuffl": [36, 38], "blocksiz": [36, 38, 45, 46, 47, 168], "probability_dtyp": [36, 38], "max_mem": [36, 38], "4gb": [36, 38], "pack": [36, 38], "tempdir": [36, 38, 45, 46, 174], "rechunk_bgen": 36, "mutablemap": [36, 38, 39, 42, 43, 46, 50, 53, 68], "system": [36, 38, 39, 42, 43, 45, 46, 50, 53, 68, 174], "slice": [36, 165, 168, 169], "isel": [36, 168], "semant": [36, 168], "10_000": [36, 38], "width": [36, 38, 45, 46, 47, 174], "1_000": [36, 38], "raw": 36, "vertic": [36, 54], "horizont": 36, "target": [36, 174], "No": [36, 45, 46, 47, 52], "either": [36, 38, 39, 40, 41, 42, 44, 48, 56, 61, 62, 63, 168, 173, 174], "uint16": [36, 38], "loss": [36, 38], "precis": [36, 38, 48, 174], "alter": [36, 38, 57], "amount": [36, 38, 173], "worker": [36, 38, 173, 174], "100mb": [36, 38, 44], "optim": [36, 38, 48], "unnecessari": [36, 38], "collaps": [36, 38], "restor": [36, 38], "expens": [36, 38, 68, 173], "extra": [36, 38, 45, 46, 47, 65, 173, 174], "temporari": [36, 38, 45, 46, 174], "bi": [36, 37, 38], "metafile_path": 37, "sample_path": 37, "lock": [37, 39, 40], "persist": [37, 39, 40], "contig_dtyp": 37, "gp_dtype": 37, "companion": [37, 168], "offset": [37, 166, 174], "metafil": 37, "slower": [37, 39, 40], "subsequ": 37, "fetch": 37, "prefer": 37, "embed": 37, "synchron": [37, 39, 40], "concurr": [37, 39, 40], "from_arrai": [37, 39, 40], "latest": [37, 38, 39, 40, 66], "consider": [37, 39, 40, 174], "metadata": [37, 173, 174], "variant_id_spec": [37, 40, 65], "variant_contig_spec": [37, 40, 65, 66, 70, 165, 166, 167], "variant_position_spec": [37, 40, 65, 70, 165, 166], "variant_allele_spec": [37, 40, 65, 70], "sample_id_spec": [37, 40, 57, 64, 65, 70, 94], "call_dosage_mask_spec": 37, "call_genotype_probability_mask_spec": 37, "origin": [38, 48, 61, 62, 63, 111, 168, 170], "experi": 38, "larger": [38, 45, 46, 47, 65, 168, 173], "fairli": 38, "aggress": 38, "lazili": [38, 168], "slow": [38, 46], "serial": 38, "bed_path": [39, 40, 41, 42], "bim_path": [39, 40, 41, 42], "fam_path": [39, 40, 41, 42], "fam_sep": [39, 40], "bim_sep": [39, 40], "bim_int_contig": [39, 40], "storage_opt": [39, 43, 44, 53, 68, 174], "suffix": [39, 40, 41, 42, 44], "bed": [39, 40, 41, 42, 173], "fam": [39, 40, 41, 42, 173], "bim": [39, 40, 41, 42, 173], "intern": [39, 40, 41, 42, 168, 173], "conjunct": [39, 40, 41, 42, 168], "delimit": [39, 40], "interpret": [39, 40, 70, 111, 120], "encount": [39, 40, 174], "plain": [39, 40], "lead": [39, 40], "upward": [39, 40], "10x": [39, 40], "backend": [39, 43, 44, 45, 46, 47, 53, 68, 168, 174], "fsspec": [39, 43, 44, 45, 46, 47, 53, 68, 174], "a1": 40, "a2": 40, "someth": [40, 51, 52, 168, 173], "www": [40, 66], "cog": 40, "ax_allel": 40, "dimension": [40, 56], "accompani": 40, "sample_family_id": [40, 41], "fid": [40, 41], "sample_member_id": [40, 41], "sample_paternal_id": [40, 41], "father": [40, 41, 59], "sample_maternal_id": [40, 41], "mother": [40, 41, 59], "sample_sex": [40, 41], "code": [40, 41, 168, 170, 173, 174], "male": [40, 41], "femal": [40, 41], "sample_phenotyp": [40, 41], "taken": 41, "url": [43, 47, 174], "concaten": [43, 46, 89, 139, 174], "vcf_path": 44, "index_path": 44, "num_part": [44, 174], "target_part_s": [44, 45, 46, 49, 174], "partit": [44, 70, 170], "bcf": [44, 45, 46, 47, 49, 174], "csi": [44, 45, 46, 47, 49, 174], "bgzf": 44, "boundari": 44, "desir": [44, 45, 46, 47, 49, 66, 173, 174], "abbrevi": 44, "100_000_000": 44, "neither": 44, "autoshuffl": [45, 46, 47], "tempdir_storage_opt": [45, 46], "mixed_ploidi": [45, 46, 47, 168, 174], "truncate_cal": [45, 46, 47, 174], "max_alt_allel": [45, 46, 47], "exclude_field": [45, 46, 47], "field_def": [45, 46, 47, 65, 174], "delet": [45, 46], "pick": [45, 46, 49], "sequenti": [45, 46, 48, 49, 174], "extract": [45, 46, 47, 49, 168, 173], "prioriti": [45, 46, 49, 173], "nest": [45, 46, 47], "dictionari": [45, 46, 47, 65, 70, 169], "overrid": [45, 46, 47, 65, 174], "basi": [45, 46, 47], "evenli": [45, 46, 174], "divis": [45, 46], "sentinel": [45, 46, 47, 168], "incomplet": [45, 46, 47, 174], "prefix": [45, 46, 47], "wildcard": [45, 46, 47], "permit": [45, 46, 47], "definit": [45, 46, 47, 65, 170], "hq": [45, 46, 47, 65], "haplotyp": [45, 46, 47, 65], "spec": [45, 46, 47, 65], "samtool": [45, 46, 47, 65], "ht": [45, 46, 47, 65], "pdf": [45, 46, 47, 65], "carri": [46, 49], "concat_zarr": [46, 174], "lower": [46, 47, 77, 174], "cost": [46, 47, 173], "becom": [46, 47], "ratio": [46, 47, 109, 168], "proport": [46, 47, 133], "n_ploidi": [46, 47, 61, 62, 63, 70, 168], "mainli": [46, 47], "chunk_siz": [46, 47], "retain": 46, "output_storage_opt": 47, "decreas": 47, "dictat": 48, "decim": [48, 174], "expon": 48, "5e": 48, "throughput": 48, "speed": [48, 174], "mb": [48, 173], "appl": 48, "m1": 48, "accord": 48, "onc": [48, 168, 173], "post": 48, "extern": 48, "bgzip": [48, 174], "bcftool": [48, 174], "tabix": [48, 174], "sy": 48, "stdout": 48, "textio": [48, 50], "scratch": [48, 50], "variant_scor": [51, 52, 159], "spars": [51, 52, 54], "linkag": [51, 52, 69], "disequilibrium": [51, 52], "roger": 51, "huff": 51, "r2": [51, 52, 54], "exce": [51, 69, 174], "below": [51, 52, 168], "almost": [51, 52, 168], "priorit": [51, 52, 159], "variant_score_spec": [51, 52], "upper": 51, "triangl": 51, "coo": 51, "cmp": 51, "prune": [52, 93], "maxim": [52, 54], "mi": 52, "maximal_independent_set": 52, "comparison": [52, 56], "anyth": 52, "pruned_d": 52, "kwarg": [53, 66, 68, 173], "thin": [53, 68], "wrapper": [53, 68, 174], "open_zarr": [53, 173], "sensibl": [53, 68], "pipelin": [53, 68, 168], "impli": 54, "discuss": [54, 169, 170, 172], "ld_prune_index_to_drop_spec": 54, "individual_heterozygos": 55, "stat_observed_heterozygosity_spec": 55, "intev": 55, "stat_observed_heterozygos": [55, 131], "euclidean": 56, "split_everi": 56, "devic": 56, "distanc": [56, 166, 167], "illustr": [56, 168, 173], "let": [56, 173], "v0": 56, "v1": 56, "v2": 56, "v3": 56, "symmetr": 56, "vi": 56, "vj": 56, "correl": [56, 111], "depth": [56, 64], "recurs": 56, "aggreg": [56, 168, 173], "reduct": [56, 66, 97], "heurist": 56, "global": 56, "architectur": 56, "ith": 56, "jth": 56, "da": 56, "44948974": 56, "69041576": 56, "47722558": 56, "44089210e": 56, "62956526e": 56, "82353505e": 56, "00000000e": 56, "14285714e": 56, "parent_id_spec": [57, 64], "u2": [57, 61, 62, 63, 64, 168, 169], "tripl": [58, 132], "fst": [58, 114, 168], "stat_pbs_spec": 58, "n_cohort": 58, "cohort_nam": [58, 168], "co_": 58, "cohorts_0": [58, 114, 123, 132, 168], "cohorts_1": [58, 114, 123, 132, 168], "cohorts_2": [58, 132], "stat_pb": [58, 132], "co_0": 58, "co_1": 58, "co_2": 58, "160898": 58, "maf": 59, "sample_pc": 59, "pc": [59, 96, 112], "conomo": 59, "sister": 59, "brother": 59, "daughter": 59, "son": 59, "grandmoth": 59, "grandfath": 59, "granddaught": 59, "grandson": 59, "aunt": 59, "uncl": 59, "niec": 59, "nephew": 59, "cousin": 59, "half": [59, 61, 62, 63, 69, 166], "sxvxd": 59, "sxpc": 59, "sample_pca_projection_spec": 59, "genesi": 59, "pc_relate_phi_spec": 59, "arraylik": 59, "matthew": [59, 61, 62, 63, 69], "alexand": 59, "reiner": 59, "timothi": 59, "thornton": 59, "stat_hamilton_kerr_tau": [60, 61, 62, 63, 69, 120], "contribut": [60, 61, 62, 63, 69, 120, 133, 170], "manipul": [60, 168], "clonal": [60, 61, 62, 63], "reproduct": [60, 61, 62, 63, 69, 120], "stat_hamilton_kerr_tau_spec": [60, 61, 62, 63, 69, 119], "stat_pedigree_contribution_spec": 60, "odd": 60, "s4": [60, 64, 69, 169, 173], "s5": [60, 169, 173], "stat_pedigree_contribut": [60, 133], "stat_hamilton_kerr_lambda": [61, 62, 63, 69, 119], "hamilton": [61, 62, 63, 69], "kerr": [61, 62, 63, 69], "suitabl": [61, 62, 63, 69, 169, 173], "sexual": [61, 62, 63, 69, 120], "stat_hamilton_kerr_lambda_spec": [61, 62, 63, 69, 120], "unrecord": [61, 62, 63, 69], "gamet": [61, 62, 63, 120], "stat_pedigree_inbreeding_spec": 61, "minim": 61, "_i": 61, "_": 61, "ii": 61, "k_i": 61, "greater": [61, 62, 63], "inbr": [61, 62, 63], "stat_pedigree_inbreed": [61, 134], "somat": [61, 63], "unreduc": [61, 62, 63], "tetraploid": [61, 62, 63, 174], "07222222": 61, "homologu": [61, 63, 119], "richard": [61, 62, 63, 69], "851": [61, 62, 63, 69], "860": [61, 62, 63, 69], "stat_pedigree_inverse_kinship_spec": 62, "stat_pedigree_inverse_kinship": [62, 135], "stat_pedigree_inverse_relationship": [62, 136], "40112994": 62, "06779661": 62, "stat_genomic_kinship_spec": 63, "stat_pedigree_kinship_spec": 63, "loop": 63, "inconsist": 63, "topolog": 63, "children": [63, 64], "oppos": 63, "225": 63, "425": 63, "30416667": 63, "toma": 63, "kai": 63, "molecular": 63, "ecologi": 63, "4121": 63, "4135": 63, "ancestor_depth": 64, "descendant_depth": 64, "sel_samples_0": 64, "sel_samples_1": 64, "update_parent_id": 64, "drop_par": 64, "inclus": [64, 91, 165, 174], "ancestor": 64, "descend": 64, "ds1": 64, "ds3": 64, "call_genotype_phased_spec": [65, 70], "variant_block_s": 66, "sample_block_s": 66, "transform": [66, 174], "techniqu": 66, "subtract": 66, "residu": 66, "preprint": 66, "simpler": [66, 170], "technic": 66, "overview": [66, 170], "stage": [66, 97, 98, 99], "involv": [66, 174], "defini": 66, "whichev": 66, "split": [66, 174], "datas": 66, "apriori": 66, "rescal": 66, "stdev": 66, "experiment": 66, "binari": 66, "yet": 66, "outcom": [66, 97, 98, 99], "regenie_base_predict": [66, 97], "regenie_base_prediction_spec": 66, "regenie_meta_predict": [66, 99], "train": [66, 99], "regenie_meta_prediction_spec": 66, "regenie_loco_predict": [66, 98], "loco": [66, 98], "held": [66, 98], "regenie_loco_prediction_spec": 66, "n_contig": [66, 70, 164, 166, 167, 168, 169], "n_covari": 66, "n_trait": 66, "randomst": 66, "sample_covari": 66, "sample_trait": 66, "26kb": [66, 169], "20kb": 66, "4588": 66, "3734": 66, "4kb": [66, 168], "4886": 66, "mbatchou": 66, "barnard": 66, "backman": 66, "marcketta": 66, "computation": 66, "quantit": [66, 168, 170], "biorxiv": 66, "1101": 66, "162354v2": 66, "abstract": 66, "glow": 66, "tertiari": 66, "qualiti": [67, 163, 172], "sample_n_called_spec": 67, "sample_call_rate_spec": 67, "sample_n_het_spec": 67, "sample_n_hom_ref_spec": 67, "sample_n_hom_alt_spec": 67, "sample_n_non_ref_spec": 67, "fulli": [67, 163], "classifi": [67, 163], "to_zarr": 68, "uniform": 68, "simul": [69, 70, 173], "maccluer": 69, "throughout": [69, 174], "initialis": 69, "unsign": [69, 174], "bit": [69, 170, 174], "pattern": 69, "reshap": 69, "sim": 69, "uint32": 69, "jean": 69, "john": 69, "vanderberg": 69, "oliv": 69, "ryder": 69, "zoo": 69, "biologi": 69, "147": 69, "160": 69, "li": 69, "tier": 69, "gregori": 69, "dutkowski": 69, "thoma": 69, "mcrae": 69, "speci": 69, "1271": 69, "1282": 69, "meaningless": 70, "quantiti": [70, 74, 168], "interest": 70, "overwritten": 70, "appropri": [70, 169, 173], "context": [70, 108, 168], "percentag": 70, "field_nam": 70, "field_dtyp": 70, "arraylikespec": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "default_nam": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "__doc__": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "nallel": [71, 72], "ncorrespond": [71, 72, 88, 139, 140], "kind": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 168], "ndim": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "call_dosage_mask": 73, "ndosag": 74, "recess": 74, "domin": 74, "probabilist": 74, "ncall": [76, 84], "ncomplet": 76, "na": [77, 78, 81, 101, 130], "nindic": [77, 79, 95], "call_genotype_index_mask": 78, "nto": [78, 79, 110], "nsingl": 79, "nfor": 79, "nall": 81, "call_genotype_probability_mask": 82, "nthe": [84, 99, 108, 119, 130, 146], "nmiss": 84, "nobserv": [85, 131], "cohort_allele_frequ": 88, "ncohort": 88, "ncovari": 89, "nvariabl": 89, "nwill": 89, "interval_contig_nam": [90, 165], "interval_start": [91, 165], "interval_stop": [92, 165], "stop": [92, 162, 164, 165, 166, 167], "exclus": [92, 165], "ld_prune_index_to_drop": 93, "nvariant": [93, 140], "nuniqu": 94, "pc_relate_phi": 96, "nregeni": [97, 98, 99], "npredict": 97, "regeni": [97, 98, 99, 172], "nresult": 98, "nheld": 98, "nat": 98, "belong": 101, "member": 101, "eigenvector": 108, "nin": 108, "svd": 108, "right": 108, "decomposit": [108, 109, 110], "dask_ml": [108, 109, 110], "truncatedsvd": [108, 109, 110], "components_": 108, "ni": [109, 110], "explained_variance_ratio_": 109, "eigenvalu": [110, 111], "eigendecomposit": 110, "explained_variance_": 110, "squar": 111, "root": 111, "nthese": 111, "nand": [111, 139], "onto": 112, "nrefer": 112, "simpli": [112, 173, 174], "sample_ploidi": 113, "nwith": [113, 137, 157], "fixat": 114, "chosen": 119, "nfrom": 119, "nthi": 119, "nmeiotic": 119, "asexu": [119, 120], "nsee": [119, 120], "meiotic": 119, "nnumer": 120, "nploidi": 120, "nsexual": 120, "broadli": [120, 173], "nasexu": 120, "nare": 120, "nmatch": 120, "pi": 124, "stat_genomic_kinship": 125, "ngenom": [125, 126], "npairwis": [129, 137], "outsid": 130, "nexpect": 133, "nbase": 133, "asymmetr": 133, "nelement": 133, "ndiagon": 133, "ntrait": 139, "n2d": 139, "nindex": 145, "nscenario": [145, 169], "ngener": [145, 169], "scenario": 145, "ncount": 146, "variant_ploidi": 157, "nscore": 159, "window_contig": [160, 166, 167], "window_start": [161, 164, 166, 167], "window_stop": [162, 164, 166, 167], "variant_n_called_spec": 163, "variant_call_rate_spec": 163, "variant_n_het_spec": 163, "variant_n_hom_ref_spec": 163, "variant_n_hom_alt_spec": 163, "variant_n_non_ref_spec": 163, "variant_allele_total_spec": 163, "variant_allele_frequency_spec": 163, "span": [164, 165, 166, 167, 168], "window_start_spec": [164, 165, 166, 167], "window_stop_spec": [164, 165, 166, 167], "8b": [164, 168], "act": 165, "never": [165, 166, 167], "monoton": [165, 166, 174], "interval_contig_name_spec": 165, "interval_start_spec": 165, "interval_stop_spec": 165, "window_contig_spec": [165, 166, 167], "window_start_posit": 166, "center": [166, 168], "shift": 166, "contigu": [166, 167, 168, 174], "ds_w1": 166, "192b": 166, "64b": 166, "zip": 166, "ds_w2": 166, "240b": 166, "80b": [166, 168, 173], "96b": 167, "32b": 167, "overlap": 167, "144b": 167, "48b": 167, "toolkit": 168, "advantag": [168, 174], "ecosystem": [168, 170], "cupi": [168, 173], "interfac": 168, "cuda": 168, "fit": [168, 174], "aid": 168, "workflow": [168, 170], "assai": 168, "express": 168, "might": [168, 172, 173], "visual": 168, "1mb": 168, "184b": [168, 169], "u4": 168, "s248": 168, "s249": 168, "500kb": 168, "presenc": 168, "snv": 168, "shown": [168, 173], "entir": [168, 174], "884b": 168, "20b": 168, "120b": 168, "s7": [168, 169, 173], "s8": [168, 169], "s9": [168, 169], "200b": [168, 169, 173], "18b": 168, "referen": 168, "allele_index": 168, "2b": 168, "item": 168, "summar": 168, "variou": [168, 174], "well": [168, 172, 173, 174], "integr": 168, "domain": [168, 170], "logic": 168, "s246": 168, "s247": 168, "flexibl": [168, 174], "come": 168, "abl": 168, "transit": 168, "unstack": 168, "fillna": 168, "call_rat": 168, "898": 168, "910": 168, "894": 168, "892": 168, "906": 168, "900": 168, "titl": 168, "allud": 168, "further": 168, "nearli": 168, "9kb": 168, "800b": [168, 169], "transpar": 168, "isn": 168, "workaround": [168, 174], "design": [168, 170, 172], "own": [168, 173, 174], "accomplish": 168, "analys": [168, 172], "help": [168, 174], "exploratori": 168, "advanc": 168, "ever": 168, "worri": [168, 174], "high": 168, "locat": 168, "is_heterozyg": 168, "4b": 168, "lone": 168, "aren": 168, "realli": 168, "awar": 168, "ten": 168, "africa": 168, "asia": 168, "europ": 168, "00823045": 168, "02510823": 168, "04372041": 168, "12240725": 168, "11305475": 168, "readabl": 168, "introduc": [168, 171], "accident": 168, "namespac": 168, "collis": 168, "idiom": 168, "57": [168, 173], "ds_qc": 168, "drop_dim": 168, "u1": [168, 174], "804800": 168, "063125": 168, "560000": 168, "780000": 168, "800000": 168, "840000": 168, "960000": 168, "00091611": 168, "00588756": 168, "00550994": 168, "blockwis": 168, "interchang": 168, "freeli": 168, "notabl": [168, 174], "actual": 168, "until": 168, "retriev": 168, "client": [168, 173, 174], "coerc": 168, "asarrai": 168, "63": 168, "22kb": [168, 173], "600b": [168, 169], "unbox": 168, "69": 168, "real": 168, "unchunk": 168, "leav": 168, "trade": [168, 174], "modifi": 168, "regardless": 168, "delai": [168, 173, 174], "23kb": 169, "s47": 169, "s48": 169, "s49": 169, "s45": 169, "s46": 169, "drop_var": 169, "21kb": 169, "24b": 169, "multiindex": 169, "6b": 169, "300b": 169, "658": 169, "s6": [169, 173], "s10": 169, "s11": 169, "s12": 169, "s13": 169, "s14": 169, "s15": 169, "s16": 169, "s17": 169, "s18": 169, "s19": 169, "s20": 169, "s21": 169, "s22": 169, "s23": 169, "s24": 169, "s25": 169, "s26": 169, "s27": 169, "s28": 169, "s29": 169, "s30": 169, "s31": 169, "s32": 169, "s33": 169, "s34": 169, "s35": 169, "s36": 169, "s37": 169, "s38": 169, "s39": 169, "s40": 169, "s41": 169, "s42": 169, "s43": 169, "s44": 169, "3kb": 169, "400b": 169, "pos0": 169, "32kb": [169, 173], "792b": 169, "198b": 169, "old": 169, "analyt": 170, "framework": 170, "intend": 170, "adopt": 170, "broader": 170, "easi": 170, "down": [170, 173], "done": [170, 173, 174], "front": 170, "inspir": 170, "heavili": 170, "popular": [170, 172], "focu": 170, "chain": 170, "guid": 170, "deploy": 170, "troubleshoot": 170, "highlight": 170, "cloud": 170, "forum": 170, "repositori": 170, "review": 170, "changelog": 170, "unreleas": 170, "june": 170, "2024": 170, "2023": 170, "februari": 170, "search": 170, "2022": 171, "team": [171, 172], "announc": [171, 172], "oxford": 172, "began": 172, "collabor": 172, "earli": 172, "successor": 172, "ve": 172, "close": 172, "parti": 172, "author": 172, "cyvcf2": [172, 173, 174], "bed_read": 172, "novel": 172, "2021": 172, "uk": [172, 174], "zealand": 172, "hesit": 172, "feedback": 172, "mac": 173, "bioconda": 173, "read_x": 173, "x_to_zarr": 173, "speak": 173, "paid": 173, "newli": 173, "consolid": 173, "bgen_to_zarr": 173, "todo": 173, "count_allel": 173, "realist": 173, "my_call_genotyp": 173, "my_call_allele_count": 173, "traceback": 173, "175": 173, "115": 173, "117": 173, "172": 173, "173": 173, "174": 173, "define_variable_if_abs": 173, "176": 173, "177": 173, "178": 173, "179": 173, "279": 173, "default_variable_nam": 173, "variable_nam": 173, "func": 173, "277": 173, "278": 173, "280": 173, "282": 173, "plu": 173, "unchang": 173, "thrown": 173, "catch_warn": 173, "categori": 173, "__name__": [173, 174], "messag": 173, "mergewarn": 173, "my_variant_allele_count": 173, "12kb": 173, "405": 173, "properti": 173, "difficult": 173, "briefli": 173, "critic": 173, "finish": 173, "alt_allele_count": 173, "ndindex": 173, "njit": 173, "ml": 173, "remot": 173, "thread": [173, 174], "kubernet": 173, "jobqueu": 173, "pb": 173, "slurm": 173, "moab": 173, "sge": 173, "lsf": 173, "htcondor": 173, "aw": 173, "gcp": [173, 174], "mpi": 173, "coil": 173, "research": 173, "institut": 173, "job": [173, 174], "schedul": [173, 174], "lf": 173, "connect": 173, "repl": 173, "adjust": 173, "fly": 173, "login": 173, "submiss": 173, "privileg": 173, "dask_jobqueu": 173, "lsfcluster": 173, "16gb": 173, "myproject": 173, "queue": 173, "myqueu": 173, "walltim": 173, "use_stdin": 173, "lsf_unit": 173, "job_script_proloug": 173, "gracefulli": 173, "reach": 173, "wallclock": 173, "shorter": [173, 174], "worker_extra_arg": 173, "lifetim": 173, "350m": 173, "stagger": 173, "5m": 173, "view": 173, "dashboard": [173, 174], "address": 173, "dashboard_link": 173, "launch": 173, "At": 173, "visibl": 173, "adapt": 173, "queu": 173, "prevent": 173, "idl": 173, "short": 173, "wait_count": 173, "120": 173, "thousand": 173, "cycl": 173, "wait": 173, "scheduler_address": 173, "constructor": 173, "8786": 173, "mydata": 173, "diagnost": 173, "progress": [173, 174], "progressbar": 173, "resourceprofil": 173, "profil": 173, "stream": 173, "bottleneck": 173, "optimize_graph": 173, "ipython": 173, "keyword": 173, "cmap": 173, "autumn": 173, "penwidth": 173, "circular": 173, "box": 173, "red": 173, "yellow": 173, "acceler": 173, "recompil": 173, "session": 173, "occasion": 173, "cython": 174, "htslib": 174, "industri": 174, "resid": 174, "amazon": 174, "googl": 174, "read_scikit_allel_vcfzarr": 174, "ceutrio": 174, "gatk3": 174, "19910": 174, "u7": 174, "max_variant_allele_length": 174, "max_variant_id_length": 174, "scene": 174, "chr": 174, "beg": 174, "partition_into_region": 174, "10108928": 174, "10108929": 174, "10207232": 174, "10207233": 174, "10027008": 174, "10027009": 174, "10043392": 174, "10043393": 174, "10141696": 174, "10141697": 174, "10174464": 174, "10174465": 174, "10190848": 174, "10190849": 174, "100_000": 174, "special": 174, "One": 174, "abil": 174, "word": 174, "honor": 174, "wherea": 174, "solut": 174, "slight": 174, "s3f": 174, "gcsf": 174, "credenti": 174, "reli": 174, "offer": 174, "lot": 174, "tri": 174, "benefit": 174, "delta": 174, "numcodec": 174, "codec": 174, "explor": 174, "know": 174, "fixedscaleoffset": 174, "call_d": 174, "f4": 174, "quantiz": 174, "float16": 174, "bitround": 174, "mechan": 174, "debug": 174, "four": 174, "polysom": 174, "polyploidi": 174, "took": 174, "hour": 174, "vcpu": 174, "128gb": 174, "e2": 174, "ftp": 174, "mkdir": 174, "wget": 174, "1000genom": 174, "ebi": 174, "vol1": 174, "20130502": 174, "phase3_shapeit2_mvncall_integrated_v5b": 174, "__main__": 174, "n_worker": 174, "threads_per_work": 174, "multiprocess": 174, "overcommit": 174, "coars": 174, "grain": 174, "minut": 174, "81271745": 174, "2504": 174, "max_alt_alleles_seen": 174}, "objects": {"sgkit": [[7, 0, 1, "", "Fst"], [8, 0, 1, "", "Garud_H"], [9, 0, 1, "", "Tajimas_D"], [10, 0, 1, "", "Weir_Goudet_beta"], [11, 0, 1, "", "call_allele_frequencies"], [12, 0, 1, "", "cohort_allele_frequencies"], [13, 0, 1, "", "convert_call_to_index"], [14, 0, 1, "", "convert_probability_to_call"], [15, 0, 1, "", "count_call_alleles"], [16, 0, 1, "", "count_cohort_alleles"], [17, 0, 1, "", "count_variant_alleles"], [18, 0, 1, "", "count_variant_genotypes"], [19, 0, 1, "", "display_genotypes"], [20, 0, 1, "", "display_pedigree"], [21, 0, 1, "", "divergence"], [22, 0, 1, "", "diversity"], [23, 0, 1, "", "filter_partial_calls"], [24, 0, 1, "", "genee"], [25, 0, 1, "", "genomic_relationship"], [26, 0, 1, "", "gwas_linear_regression"], [27, 0, 1, "", "hardy_weinberg_test"], [28, 0, 1, "", "hybrid_inverse_relationship"], [29, 0, 1, "", "hybrid_relationship"], [30, 0, 1, "", "identity_by_state"], [31, 0, 1, "", "individual_heterozygosity"], [32, 0, 1, "", "infer_call_ploidy"], [33, 0, 1, "", "infer_sample_ploidy"], [34, 0, 1, "", "infer_variant_ploidy"], [35, 0, 1, "", "invert_relationship_matrix"], [51, 0, 1, "", "ld_matrix"], [52, 0, 1, "", "ld_prune"], [53, 0, 1, "", "load_dataset"], [54, 0, 1, "", "maximal_independent_set"], [55, 0, 1, "", "observed_heterozygosity"], [56, 0, 1, "", "pairwise_distance"], [57, 0, 1, "", "parent_indices"], [58, 0, 1, "", "pbs"], [59, 0, 1, "", "pc_relate"], [60, 0, 1, "", "pedigree_contribution"], [61, 0, 1, "", "pedigree_inbreeding"], [62, 0, 1, "", "pedigree_inverse_kinship"], [63, 0, 1, "", "pedigree_kinship"], [64, 0, 1, "", "pedigree_sel"], [65, 0, 1, "", "read_scikit_allel_vcfzarr"], [66, 0, 1, "", "regenie"], [67, 0, 1, "", "sample_stats"], [68, 0, 1, "", "save_dataset"], [69, 0, 1, "", "simulate_genedrop"], [70, 0, 1, "", "simulate_genotype_call_dataset"], [163, 0, 1, "", "variant_stats"], [164, 0, 1, "", "window_by_genome"], [165, 0, 1, "", "window_by_interval"], [166, 0, 1, "", "window_by_position"], [167, 0, 1, "", "window_by_variant"]], "sgkit.io.bgen": [[36, 0, 1, "", "bgen_to_zarr"], [37, 0, 1, "", "read_bgen"], [38, 0, 1, "", "rechunk_bgen"]], "sgkit.io.plink": [[39, 0, 1, "", "plink_to_zarr"], [40, 0, 1, "", "read_plink"], [41, 0, 1, "", "write_plink"], [42, 0, 1, "", "zarr_to_plink"]], "sgkit.io.vcf": [[43, 0, 1, "", "concat_zarrs"], [44, 0, 1, "", "partition_into_regions"], [45, 0, 1, "", "read_vcf"], [46, 0, 1, "", "vcf_to_zarr"], [47, 0, 1, "", "vcf_to_zarrs"], [48, 0, 1, "", "write_vcf"], [49, 0, 1, "", "zarr_array_sizes"], [50, 0, 1, "", "zarr_to_vcf"]], "sgkit.variables": [[71, 1, 1, "", "call_allele_count_spec"], [72, 1, 1, "", "call_allele_frequency_spec"], [73, 1, 1, "", "call_dosage_mask_spec"], [74, 1, 1, "", "call_dosage_spec"], [75, 1, 1, "", "call_genotype_complete_mask_spec"], [76, 1, 1, "", "call_genotype_complete_spec"], [77, 1, 1, "", "call_genotype_fill_spec"], [78, 1, 1, "", "call_genotype_index_mask_spec"], [79, 1, 1, "", "call_genotype_index_spec"], [80, 1, 1, "", "call_genotype_mask_spec"], [81, 1, 1, "", "call_genotype_phased_spec"], [82, 1, 1, "", "call_genotype_probability_mask_spec"], [83, 1, 1, "", "call_genotype_probability_spec"], [84, 1, 1, "", "call_genotype_spec"], [85, 1, 1, "", "call_heterozygosity_spec"], [86, 1, 1, "", "call_ploidy_spec"], [87, 1, 1, "", "cohort_allele_count_spec"], [88, 1, 1, "", "cohort_allele_frequency_spec"], [89, 1, 1, "", "covariates_spec"], [90, 1, 1, "", "interval_contig_name_spec"], [91, 1, 1, "", "interval_start_spec"], [92, 1, 1, "", "interval_stop_spec"], [93, 1, 1, "", "ld_prune_index_to_drop_spec"], [94, 1, 1, "", "parent_id_spec"], [95, 1, 1, "", "parent_spec"], [96, 1, 1, "", "pc_relate_phi_spec"], [97, 1, 1, "", "regenie_base_prediction_spec"], [98, 1, 1, "", "regenie_loco_prediction_spec"], [99, 1, 1, "", "regenie_meta_prediction_spec"], [100, 1, 1, "", "sample_call_rate_spec"], [101, 1, 1, "", "sample_cohort_spec"], [102, 1, 1, "", "sample_id_spec"], [103, 1, 1, "", "sample_n_called_spec"], [104, 1, 1, "", "sample_n_het_spec"], [105, 1, 1, "", "sample_n_hom_alt_spec"], [106, 1, 1, "", "sample_n_hom_ref_spec"], [107, 1, 1, "", "sample_n_non_ref_spec"], [108, 1, 1, "", "sample_pca_component_spec"], [109, 1, 1, "", "sample_pca_explained_variance_ratio_spec"], [110, 1, 1, "", "sample_pca_explained_variance_spec"], [111, 1, 1, "", "sample_pca_loading_spec"], [112, 1, 1, "", "sample_pca_projection_spec"], [113, 1, 1, "", "sample_ploidy_spec"], [114, 1, 1, "", "stat_Fst_spec"], [115, 1, 1, "", "stat_Garud_h123_spec"], [116, 1, 1, "", "stat_Garud_h12_spec"], [117, 1, 1, "", "stat_Garud_h1_spec"], [118, 1, 1, "", "stat_Garud_h2_h1_spec"], [119, 1, 1, "", "stat_Hamilton_Kerr_lambda_spec"], [120, 1, 1, "", "stat_Hamilton_Kerr_tau_spec"], [121, 1, 1, "", "stat_Tajimas_D_spec"], [122, 1, 1, "", "stat_Weir_Goudet_beta_spec"], [123, 1, 1, "", "stat_divergence_spec"], [124, 1, 1, "", "stat_diversity_spec"], [125, 1, 1, "", "stat_genomic_kinship_spec"], [126, 1, 1, "", "stat_genomic_relationship_spec"], [127, 1, 1, "", "stat_hybrid_inverse_relationship_spec"], [128, 1, 1, "", "stat_hybrid_relationship_spec"], [129, 1, 1, "", "stat_identity_by_state_spec"], [130, 1, 1, "", "stat_inverse_relationship_spec"], [131, 1, 1, "", "stat_observed_heterozygosity_spec"], [132, 1, 1, "", "stat_pbs_spec"], [133, 1, 1, "", "stat_pedigree_contribution_spec"], [134, 1, 1, "", "stat_pedigree_inbreeding_spec"], [135, 1, 1, "", "stat_pedigree_inverse_kinship_spec"], [136, 1, 1, "", "stat_pedigree_inverse_relationship_spec"], [137, 1, 1, "", "stat_pedigree_kinship_spec"], [138, 1, 1, "", "stat_pedigree_relationship_spec"], [139, 1, 1, "", "traits_spec"], [140, 1, 1, "", "variant_allele_count_spec"], [141, 1, 1, "", "variant_allele_frequency_spec"], [142, 1, 1, "", "variant_allele_spec"], [143, 1, 1, "", "variant_allele_total_spec"], [144, 1, 1, "", "variant_call_rate_spec"], [145, 1, 1, "", "variant_contig_spec"], [146, 1, 1, "", "variant_genotype_count_spec"], [147, 1, 1, "", "variant_hwe_p_value_spec"], [148, 1, 1, "", "variant_id_spec"], [149, 1, 1, "", "variant_linreg_beta_spec"], [150, 1, 1, "", "variant_linreg_p_value_spec"], [151, 1, 1, "", "variant_linreg_t_value_spec"], [152, 1, 1, "", "variant_n_called_spec"], [153, 1, 1, "", "variant_n_het_spec"], [154, 1, 1, "", "variant_n_hom_alt_spec"], [155, 1, 1, "", "variant_n_hom_ref_spec"], [156, 1, 1, "", "variant_n_non_ref_spec"], [157, 1, 1, "", "variant_ploidy_spec"], [158, 1, 1, "", "variant_position_spec"], [159, 1, 1, "", "variant_score_spec"], [160, 1, 1, "", "window_contig_spec"], [161, 1, 1, "", "window_start_spec"], [162, 1, 1, "", "window_stop_spec"]]}, "objtypes": {"0": "py:function", "1": "py:data"}, "objnames": {"0": ["py", "function", "Python function"], "1": ["py", "data", "Python data"]}, "titleterms": {"about": 0, "api": [1, 3], "refer": [1, 6], "io": [1, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "import": [1, 4], "export": 1, "bgen": [1, 36, 37, 38, 173], "plink": [1, 39, 40, 41, 42, 173], "vcf": [1, 4, 43, 44, 45, 46, 47, 48, 49, 50, 173, 174], "read": [1, 6, 173, 174], "write": [1, 173], "dataset": [1, 3, 6, 169, 173, 174], "method": [1, 168, 169, 173], "basic": 1, "genet": [1, 168, 170, 173], "statist": [1, 170], "popul": 1, "related": [1, 6], "linkag": 1, "disequilibrium": 1, "associ": 1, "regress": 1, "miscellan": 1, "util": 1, "variabl": [1, 3, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 169, 173], "changelog": 2, "0": 2, "10": 2, "unreleas": 2, "new": [2, 169, 171], "featur": 2, "document": [2, 3], "9": 2, "24": 2, "june": 2, "2024": 2, "deprec": 2, "improv": 2, "8": 2, "1": 2, "mai": 2, "bug": 2, "fix": 2, "7": 2, "2": 2, "2023": 2, "break": 2, "chang": 2, "6": 2, "februari": 2, "contribut": 3, "sgkit": [3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 170, 172, 173, 174], "tabl": [3, 168, 170, 173, 174], "content": [3, 168, 170, 173, 174], "discuss": 3, "forum": 3, "code": 3, "repositori": 3, "issu": 3, "develop": 3, "environ": 3, "download": [3, 4, 6, 174], "instal": [3, 168, 173, 174], "run": [3, 174], "test": [3, 169], "continu": 3, "integr": 3, "docstr": 3, "standard": 3, "pr": 3, "git": 3, "op": 3, "python": [3, 170, 173], "depend": 3, "benchmark": 3, "review": 3, "process": 3, "design": 3, "subclass": 3, "type": 3, "delai": 3, "invari": 3, "check": 3, "mix": [3, 174], "ploidi": [3, 174], "numba": [3, 173], "guvector": 3, "usag": [3, 174], "namespac": 3, "gwa": 4, "tutori": [4, 6], "public": 4, "1000": [4, 174], "genom": [4, 6, 169, 174], "data": [4, 6, 168, 173, 174], "from": [4, 169], "get": [4, 168, 169], "know": 4, "our": 4, "ad": [4, 169, 173], "column": 4, "field": 4, "queri": 4, "function": 4, "qualiti": 4, "control": 4, "let": 4, "": 4, "do": [4, 169], "confound": 4, "exampl": [5, 174], "pig": 6, "pedigre": 6, "work": [6, 173], "relationship": 6, "The": 6, "vanraden": 6, "grm": 6, "A": 6, "better": 6, "estim": 6, "ancestr": 6, "allel": 6, "frequenc": 6, "weir": 6, "goudet": 6, "hybrid": 6, "matric": 6, "fst": 7, "garud_h": 8, "tajimas_d": 9, "weir_goudet_beta": 10, "call_allele_frequ": 11, "cohort_allele_frequ": 12, "convert_call_to_index": 13, "convert_probability_to_cal": 14, "count_call_allel": 15, "count_cohort_allel": 16, "count_variant_allel": 17, "count_variant_genotyp": 18, "display_genotyp": 19, "display_pedigre": 20, "diverg": 21, "divers": 22, "filter_partial_cal": 23, "gene": 24, "genomic_relationship": 25, "gwas_linear_regress": 26, "hardy_weinberg_test": 27, "hybrid_inverse_relationship": 28, "hybrid_relationship": 29, "identity_by_st": 30, "individual_heterozygos": 31, "infer_call_ploidi": 32, "infer_sample_ploidi": 33, "infer_variant_ploidi": 34, "invert_relationship_matrix": 35, "bgen_to_zarr": 36, "read_bgen": 37, "rechunk_bgen": 38, "plink_to_zarr": 39, "read_plink": 40, "write_plink": 41, "zarr_to_plink": 42, "concat_zarr": 43, "partition_into_region": 44, "read_vcf": 45, "vcf_to_zarr": [46, 47], "write_vcf": 48, "zarr_array_s": 49, "zarr_to_vcf": 50, "ld_matrix": 51, "ld_prune": 52, "load_dataset": 53, "maximal_independent_set": 54, "observed_heterozygos": 55, "pairwise_dist": 56, "parent_indic": 57, "pb": 58, "pc_relat": 59, "pedigree_contribut": 60, "pedigree_inbreed": 61, "pedigree_inverse_kinship": 62, "pedigree_kinship": 63, "pedigree_sel": 64, "read_scikit_allel_vcfzarr": 65, "regeni": 66, "sample_stat": 67, "save_dataset": 68, "simulate_genedrop": 69, "simulate_genotype_call_dataset": 70, "call_allele_count_spec": 71, "call_allele_frequency_spec": 72, "call_dosage_mask_spec": 73, "call_dosage_spec": 74, "call_genotype_complete_mask_spec": 75, "call_genotype_complete_spec": 76, "call_genotype_fill_spec": 77, "call_genotype_index_mask_spec": 78, "call_genotype_index_spec": 79, "call_genotype_mask_spec": 80, "call_genotype_phased_spec": 81, "call_genotype_probability_mask_spec": 82, "call_genotype_probability_spec": 83, "call_genotype_spec": 84, "call_heterozygosity_spec": 85, "call_ploidy_spec": 86, "cohort_allele_count_spec": 87, "cohort_allele_frequency_spec": 88, "covariates_spec": 89, "interval_contig_name_spec": 90, "interval_start_spec": 91, "interval_stop_spec": 92, "ld_prune_index_to_drop_spec": 93, "parent_id_spec": 94, "parent_spec": 95, "pc_relate_phi_spec": 96, "regenie_base_prediction_spec": 97, "regenie_loco_prediction_spec": 98, "regenie_meta_prediction_spec": 99, "sample_call_rate_spec": 100, "sample_cohort_spec": 101, "sample_id_spec": 102, "sample_n_called_spec": 103, "sample_n_het_spec": 104, "sample_n_hom_alt_spec": 105, "sample_n_hom_ref_spec": 106, "sample_n_non_ref_spec": 107, "sample_pca_component_spec": 108, "sample_pca_explained_variance_ratio_spec": 109, "sample_pca_explained_variance_spec": 110, "sample_pca_loading_spec": 111, "sample_pca_projection_spec": 112, "sample_ploidy_spec": 113, "stat_fst_spec": 114, "stat_garud_h123_spec": 115, "stat_garud_h12_spec": 116, "stat_garud_h1_spec": 117, "stat_garud_h2_h1_spec": 118, "stat_hamilton_kerr_lambda_spec": 119, "stat_hamilton_kerr_tau_spec": 120, "stat_tajimas_d_spec": 121, "stat_weir_goudet_beta_spec": 122, "stat_divergence_spec": 123, "stat_diversity_spec": 124, "stat_genomic_kinship_spec": 125, "stat_genomic_relationship_spec": 126, "stat_hybrid_inverse_relationship_spec": 127, "stat_hybrid_relationship_spec": 128, "stat_identity_by_state_spec": 129, "stat_inverse_relationship_spec": 130, "stat_observed_heterozygosity_spec": 131, "stat_pbs_spec": 132, "stat_pedigree_contribution_spec": 133, "stat_pedigree_inbreeding_spec": 134, "stat_pedigree_inverse_kinship_spec": 135, "stat_pedigree_inverse_relationship_spec": 136, "stat_pedigree_kinship_spec": 137, "stat_pedigree_relationship_spec": 138, "traits_spec": 139, "variant_allele_count_spec": 140, "variant_allele_frequency_spec": 141, "variant_allele_spec": 142, "variant_allele_total_spec": 143, "variant_call_rate_spec": 144, "variant_contig_spec": 145, "variant_genotype_count_spec": 146, "variant_hwe_p_value_spec": 147, "variant_id_spec": 148, "variant_linreg_beta_spec": 149, "variant_linreg_p_value_spec": 150, "variant_linreg_t_value_spec": 151, "variant_n_called_spec": 152, "variant_n_het_spec": 153, "variant_n_hom_alt_spec": 154, "variant_n_hom_ref_spec": 155, "variant_n_non_ref_spec": 156, "variant_ploidy_spec": 157, "variant_position_spec": 158, "variant_score_spec": 159, "window_contig_spec": 160, "window_start_spec": 161, "window_stop_spec": 162, "variant_stat": 163, "window_by_genom": 164, "window_by_interv": 165, "window_by_posit": 166, "window_by_vari": 167, "start": 168, "overview": 168, "structur": 168, "miss": 168, "window": 168, "cohort": 168, "chain": 168, "oper": [168, 173, 174], "chunk": [168, 174], "arrai": 168, "how": 169, "i": 169, "creat": 169, "look": 169, "summari": 169, "valu": 169, "find": 169, "definit": 169, "genotyp": 169, "subset": 169, "rang": 169, "list": 169, "sampl": 169, "defin": 169, "base": 169, "other": [169, 173], "stat": 169, "filter": 169, "variant": 169, "which": 169, "were": 169, "save": 169, "result": 169, "zarr": [169, 173, 174], "file": [169, 174], "load": 169, "toolkit": 170, "indic": 170, "introduc": 172, "user": 173, "guid": 173, "convert": [173, 174], "cloud": [173, 174], "nativ": 173, "merg": 173, "behavior": 173, "interop": 173, "librari": 173, "custom": 173, "name": 173, "convent": 173, "comput": 173, "pca": 173, "deploy": 173, "deploi": 173, "cluster": 173, "us": 173, "gpu": 173, "troubleshoot": 173, "monitor": 173, "visual": 173, "disabl": 173, "cach": 173, "highlight": 174, "multipl": 174, "partit": 174, "size": 174, "storag": 174, "compress": 174, "low": 174, "level": 174, "polyploid": 174, "convers": 174, "inspect": 174}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "scanpydoc.elegant_typehints": 1, "sphinx.ext.intersphinx": 1, "scanpydoc.autosummary_generate_imported": 1, "scanpydoc.definition_list_typed_field": 1, "scanpydoc.rtd_github_links": 1, "scanpydoc": 1, "sphinx": 57}, "alltitles": {"About": [[0, "about"]], "API reference": [[1, "api-reference"]], "IO/imports and exports": [[1, "io-imports-and-exports"]], "BGEN": [[1, "bgen"], [173, "bgen"]], "PLINK": [[1, "plink"], [173, "plink"]], "VCF (reading)": [[1, "vcf-reading"]], "VCF (writing)": [[1, "vcf-writing"]], "Dataset": [[1, "dataset"]], "Methods": [[1, "methods"], [173, "methods"]], "Basic genetics statistics": [[1, "basic-genetics-statistics"]], "Population genetic statistics": [[1, "population-genetic-statistics"]], "Relatedness": [[1, "relatedness"]], "Linkage Disequilibrium": [[1, "linkage-disequilibrium"]], "Genetic Association and Regression": [[1, "genetic-association-and-regression"]], "Miscellaneous": [[1, "miscellaneous"]], "Utilities": [[1, "utilities"]], "Variables": [[1, "variables"]], "Changelog": [[2, "changelog"]], "0.10.0 (unreleased)": [[2, "unreleased"]], "New Features": [[2, "new-features"], [2, "id1"], [2, "id4"], [2, "id8"]], "Documentation": [[2, "documentation"], [2, "id3"]], "0.9.0 (24 June 2024)": [[2, "june-2024"]], "Deprecations": [[2, "deprecations"], [2, "id5"]], "Improvements": [[2, "improvements"], [2, "id2"], [2, "id6"], [2, "id10"]], "0.8.0 (1 May 2024)": [[2, "may-2024"]], "Bug fixes": [[2, "bug-fixes"], [2, "id7"], [2, "id11"]], "0.7.0 (2 May 2023)": [[2, "may-2023"]], "Breaking changes": [[2, "breaking-changes"], [2, "id9"]], "0.6.0 (1 February 2023)": [[2, "february-2023"]], "Contributing to sgkit": [[3, "contributing-to-sgkit"]], "Table of contents:": [[3, "table-of-contents"], [168, "table-of-contents"], [173, "table-of-contents"], [174, "table-of-contents"]], "Discussion forums": [[3, "discussion-forums"]], "Code repositories": [[3, "code-repositories"]], "Issues": [[3, "issues"]], "Development environment": [[3, "development-environment"]], "Download code": [[3, "download-code"]], "Install": [[3, "install"]], "Run tests": [[3, "run-tests"]], "Contributing to code": [[3, "contributing-to-code"]], "Continuous Integration": [[3, "continuous-integration"]], "Test": [[3, "test"]], "Docstrings": [[3, "docstrings"]], "Coding standards": [[3, "coding-standards"]], "PR/Git ops": [[3, "pr-git-ops"]], "Python dependencies": [[3, "python-dependencies"]], "Contributing to documentation": [[3, "contributing-to-documentation"]], "Benchmarks": [[3, "benchmarks"]], "Review process": [[3, "review-process"]], "Design discussions": [[3, "design-discussions"]], "Dataset subclassing": [[3, "dataset-subclassing"]], "Dataset API typing": [[3, "dataset-api-typing"]], "Dataset variables": [[3, "dataset-variables"]], "Delayed invariant checks": [[3, "delayed-invariant-checks"]], "Mixed ploidy": [[3, "mixed-ploidy"]], "Numba guvectorize usage": [[3, "numba-guvectorize-usage"]], "API namespace": [[3, "api-namespace"]], "GWAS Tutorial": [[4, "gwas-tutorial"]], "Download public 1000 Genomes data": [[4, "download-public-1000-genomes-data"]], "Importing data from VCF": [[4, "importing-data-from-vcf"]], "Getting to know our data": [[4, "getting-to-know-our-data"]], "Adding column fields": [[4, "adding-column-fields"]], "Query functions": [[4, "query-functions"]], "Quality control": [[4, "quality-control"]], "Let\u2019s do a GWAS!": [[4, "let-s-do-a-gwas"]], "Confounded!": [[4, "confounded"]], "Examples": [[5, "examples"]], "Relatedness Tutorial": [[6, "relatedness-tutorial"]], "Download the pig dataset": [[6, "download-the-pig-dataset"]], "Reading pedigree data": [[6, "reading-pedigree-data"]], "Working with pedigree data": [[6, "working-with-pedigree-data"]], "Pedigree relationships": [[6, "pedigree-relationships"]], "Genomic relationships": [[6, "genomic-relationships"]], "The VanRaden GRM": [[6, "the-vanraden-grm"]], "A better estimate of ancestral allele frequencies": [[6, "a-better-estimate-of-ancestral-allele-frequencies"]], "Weir-Goudet GRM": [[6, "weir-goudet-grm"]], "Hybrid relationship matrices": [[6, "hybrid-relationship-matrices"]], "References": [[6, "references"]], "sgkit.Fst": [[7, "sgkit-fst"]], "sgkit.Garud_H": [[8, "sgkit-garud-h"]], "sgkit.Tajimas_D": [[9, "sgkit-tajimas-d"]], "sgkit.Weir_Goudet_beta": [[10, "sgkit-weir-goudet-beta"]], "sgkit.call_allele_frequencies": [[11, "sgkit-call-allele-frequencies"]], "sgkit.cohort_allele_frequencies": [[12, "sgkit-cohort-allele-frequencies"]], "sgkit.convert_call_to_index": [[13, "sgkit-convert-call-to-index"]], "sgkit.convert_probability_to_call": [[14, "sgkit-convert-probability-to-call"]], "sgkit.count_call_alleles": [[15, "sgkit-count-call-alleles"]], "sgkit.count_cohort_alleles": [[16, "sgkit-count-cohort-alleles"]], "sgkit.count_variant_alleles": [[17, "sgkit-count-variant-alleles"]], "sgkit.count_variant_genotypes": [[18, "sgkit-count-variant-genotypes"]], "sgkit.display_genotypes": [[19, "sgkit-display-genotypes"]], "sgkit.display_pedigree": [[20, "sgkit-display-pedigree"]], "sgkit.divergence": [[21, "sgkit-divergence"]], "sgkit.diversity": [[22, "sgkit-diversity"]], "sgkit.filter_partial_calls": [[23, "sgkit-filter-partial-calls"]], "sgkit.genee": [[24, "sgkit-genee"]], "sgkit.genomic_relationship": [[25, "sgkit-genomic-relationship"]], "sgkit.gwas_linear_regression": [[26, "sgkit-gwas-linear-regression"]], "sgkit.hardy_weinberg_test": [[27, "sgkit-hardy-weinberg-test"]], "sgkit.hybrid_inverse_relationship": [[28, "sgkit-hybrid-inverse-relationship"]], "sgkit.hybrid_relationship": [[29, "sgkit-hybrid-relationship"]], "sgkit.identity_by_state": [[30, "sgkit-identity-by-state"]], "sgkit.individual_heterozygosity": [[31, "sgkit-individual-heterozygosity"]], "sgkit.infer_call_ploidy": [[32, "sgkit-infer-call-ploidy"]], "sgkit.infer_sample_ploidy": [[33, "sgkit-infer-sample-ploidy"]], "sgkit.infer_variant_ploidy": [[34, "sgkit-infer-variant-ploidy"]], "sgkit.invert_relationship_matrix": [[35, "sgkit-invert-relationship-matrix"]], "sgkit.io.bgen.bgen_to_zarr": [[36, "sgkit-io-bgen-bgen-to-zarr"]], "sgkit.io.bgen.read_bgen": [[37, "sgkit-io-bgen-read-bgen"]], "sgkit.io.bgen.rechunk_bgen": [[38, "sgkit-io-bgen-rechunk-bgen"]], "sgkit.io.plink.plink_to_zarr": [[39, "sgkit-io-plink-plink-to-zarr"]], "sgkit.io.plink.read_plink": [[40, "sgkit-io-plink-read-plink"]], "sgkit.io.plink.write_plink": [[41, "sgkit-io-plink-write-plink"]], "sgkit.io.plink.zarr_to_plink": [[42, "sgkit-io-plink-zarr-to-plink"]], "sgkit.io.vcf.concat_zarrs": [[43, "sgkit-io-vcf-concat-zarrs"]], "sgkit.io.vcf.partition_into_regions": [[44, "sgkit-io-vcf-partition-into-regions"]], "sgkit.io.vcf.read_vcf": [[45, "sgkit-io-vcf-read-vcf"]], "sgkit.io.vcf.vcf_to_zarr": [[46, "sgkit-io-vcf-vcf-to-zarr"]], "sgkit.io.vcf.vcf_to_zarrs": [[47, "sgkit-io-vcf-vcf-to-zarrs"]], "sgkit.io.vcf.write_vcf": [[48, "sgkit-io-vcf-write-vcf"]], "sgkit.io.vcf.zarr_array_sizes": [[49, "sgkit-io-vcf-zarr-array-sizes"]], "sgkit.io.vcf.zarr_to_vcf": [[50, "sgkit-io-vcf-zarr-to-vcf"]], "sgkit.ld_matrix": [[51, "sgkit-ld-matrix"]], "sgkit.ld_prune": [[52, "sgkit-ld-prune"]], "sgkit.load_dataset": [[53, "sgkit-load-dataset"]], "sgkit.maximal_independent_set": [[54, "sgkit-maximal-independent-set"]], "sgkit.observed_heterozygosity": [[55, "sgkit-observed-heterozygosity"]], "sgkit.pairwise_distance": [[56, "sgkit-pairwise-distance"]], "sgkit.parent_indices": [[57, "sgkit-parent-indices"]], "sgkit.pbs": [[58, "sgkit-pbs"]], "sgkit.pc_relate": [[59, "sgkit-pc-relate"]], "sgkit.pedigree_contribution": [[60, "sgkit-pedigree-contribution"]], "sgkit.pedigree_inbreeding": [[61, "sgkit-pedigree-inbreeding"]], "sgkit.pedigree_inverse_kinship": [[62, "sgkit-pedigree-inverse-kinship"]], "sgkit.pedigree_kinship": [[63, "sgkit-pedigree-kinship"]], "sgkit.pedigree_sel": [[64, "sgkit-pedigree-sel"]], "sgkit.read_scikit_allel_vcfzarr": [[65, "sgkit-read-scikit-allel-vcfzarr"]], "sgkit.regenie": [[66, "sgkit-regenie"]], "sgkit.sample_stats": [[67, "sgkit-sample-stats"]], "sgkit.save_dataset": [[68, "sgkit-save-dataset"]], "sgkit.simulate_genedrop": [[69, "sgkit-simulate-genedrop"]], "sgkit.simulate_genotype_call_dataset": [[70, "sgkit-simulate-genotype-call-dataset"]], "sgkit.variables.call_allele_count_spec": [[71, "sgkit-variables-call-allele-count-spec"]], "sgkit.variables.call_allele_frequency_spec": [[72, "sgkit-variables-call-allele-frequency-spec"]], "sgkit.variables.call_dosage_mask_spec": [[73, "sgkit-variables-call-dosage-mask-spec"]], "sgkit.variables.call_dosage_spec": [[74, "sgkit-variables-call-dosage-spec"]], "sgkit.variables.call_genotype_complete_mask_spec": [[75, "sgkit-variables-call-genotype-complete-mask-spec"]], "sgkit.variables.call_genotype_complete_spec": [[76, "sgkit-variables-call-genotype-complete-spec"]], "sgkit.variables.call_genotype_fill_spec": [[77, "sgkit-variables-call-genotype-fill-spec"]], "sgkit.variables.call_genotype_index_mask_spec": [[78, "sgkit-variables-call-genotype-index-mask-spec"]], "sgkit.variables.call_genotype_index_spec": [[79, "sgkit-variables-call-genotype-index-spec"]], "sgkit.variables.call_genotype_mask_spec": [[80, "sgkit-variables-call-genotype-mask-spec"]], "sgkit.variables.call_genotype_phased_spec": [[81, "sgkit-variables-call-genotype-phased-spec"]], "sgkit.variables.call_genotype_probability_mask_spec": [[82, "sgkit-variables-call-genotype-probability-mask-spec"]], "sgkit.variables.call_genotype_probability_spec": [[83, "sgkit-variables-call-genotype-probability-spec"]], "sgkit.variables.call_genotype_spec": [[84, "sgkit-variables-call-genotype-spec"]], "sgkit.variables.call_heterozygosity_spec": [[85, "sgkit-variables-call-heterozygosity-spec"]], "sgkit.variables.call_ploidy_spec": [[86, "sgkit-variables-call-ploidy-spec"]], "sgkit.variables.cohort_allele_count_spec": [[87, "sgkit-variables-cohort-allele-count-spec"]], "sgkit.variables.cohort_allele_frequency_spec": [[88, "sgkit-variables-cohort-allele-frequency-spec"]], "sgkit.variables.covariates_spec": [[89, "sgkit-variables-covariates-spec"]], "sgkit.variables.interval_contig_name_spec": [[90, "sgkit-variables-interval-contig-name-spec"]], "sgkit.variables.interval_start_spec": [[91, "sgkit-variables-interval-start-spec"]], "sgkit.variables.interval_stop_spec": [[92, "sgkit-variables-interval-stop-spec"]], "sgkit.variables.ld_prune_index_to_drop_spec": [[93, "sgkit-variables-ld-prune-index-to-drop-spec"]], "sgkit.variables.parent_id_spec": [[94, "sgkit-variables-parent-id-spec"]], "sgkit.variables.parent_spec": [[95, "sgkit-variables-parent-spec"]], "sgkit.variables.pc_relate_phi_spec": [[96, "sgkit-variables-pc-relate-phi-spec"]], "sgkit.variables.regenie_base_prediction_spec": [[97, "sgkit-variables-regenie-base-prediction-spec"]], "sgkit.variables.regenie_loco_prediction_spec": [[98, "sgkit-variables-regenie-loco-prediction-spec"]], "sgkit.variables.regenie_meta_prediction_spec": [[99, "sgkit-variables-regenie-meta-prediction-spec"]], "sgkit.variables.sample_call_rate_spec": [[100, "sgkit-variables-sample-call-rate-spec"]], "sgkit.variables.sample_cohort_spec": [[101, "sgkit-variables-sample-cohort-spec"]], "sgkit.variables.sample_id_spec": [[102, "sgkit-variables-sample-id-spec"]], "sgkit.variables.sample_n_called_spec": [[103, "sgkit-variables-sample-n-called-spec"]], "sgkit.variables.sample_n_het_spec": [[104, "sgkit-variables-sample-n-het-spec"]], "sgkit.variables.sample_n_hom_alt_spec": [[105, "sgkit-variables-sample-n-hom-alt-spec"]], "sgkit.variables.sample_n_hom_ref_spec": [[106, "sgkit-variables-sample-n-hom-ref-spec"]], "sgkit.variables.sample_n_non_ref_spec": [[107, "sgkit-variables-sample-n-non-ref-spec"]], "sgkit.variables.sample_pca_component_spec": [[108, "sgkit-variables-sample-pca-component-spec"]], "sgkit.variables.sample_pca_explained_variance_ratio_spec": [[109, "sgkit-variables-sample-pca-explained-variance-ratio-spec"]], "sgkit.variables.sample_pca_explained_variance_spec": [[110, "sgkit-variables-sample-pca-explained-variance-spec"]], "sgkit.variables.sample_pca_loading_spec": [[111, "sgkit-variables-sample-pca-loading-spec"]], "sgkit.variables.sample_pca_projection_spec": [[112, "sgkit-variables-sample-pca-projection-spec"]], "sgkit.variables.sample_ploidy_spec": [[113, "sgkit-variables-sample-ploidy-spec"]], "sgkit.variables.stat_Fst_spec": [[114, "sgkit-variables-stat-fst-spec"]], "sgkit.variables.stat_Garud_h123_spec": [[115, "sgkit-variables-stat-garud-h123-spec"]], "sgkit.variables.stat_Garud_h12_spec": [[116, "sgkit-variables-stat-garud-h12-spec"]], "sgkit.variables.stat_Garud_h1_spec": [[117, "sgkit-variables-stat-garud-h1-spec"]], "sgkit.variables.stat_Garud_h2_h1_spec": [[118, "sgkit-variables-stat-garud-h2-h1-spec"]], "sgkit.variables.stat_Hamilton_Kerr_lambda_spec": [[119, "sgkit-variables-stat-hamilton-kerr-lambda-spec"]], "sgkit.variables.stat_Hamilton_Kerr_tau_spec": [[120, "sgkit-variables-stat-hamilton-kerr-tau-spec"]], "sgkit.variables.stat_Tajimas_D_spec": [[121, "sgkit-variables-stat-tajimas-d-spec"]], "sgkit.variables.stat_Weir_Goudet_beta_spec": [[122, "sgkit-variables-stat-weir-goudet-beta-spec"]], "sgkit.variables.stat_divergence_spec": [[123, "sgkit-variables-stat-divergence-spec"]], "sgkit.variables.stat_diversity_spec": [[124, "sgkit-variables-stat-diversity-spec"]], "sgkit.variables.stat_genomic_kinship_spec": [[125, "sgkit-variables-stat-genomic-kinship-spec"]], "sgkit.variables.stat_genomic_relationship_spec": [[126, "sgkit-variables-stat-genomic-relationship-spec"]], "sgkit.variables.stat_hybrid_inverse_relationship_spec": [[127, "sgkit-variables-stat-hybrid-inverse-relationship-spec"]], "sgkit.variables.stat_hybrid_relationship_spec": [[128, "sgkit-variables-stat-hybrid-relationship-spec"]], "sgkit.variables.stat_identity_by_state_spec": [[129, "sgkit-variables-stat-identity-by-state-spec"]], "sgkit.variables.stat_inverse_relationship_spec": [[130, "sgkit-variables-stat-inverse-relationship-spec"]], "sgkit.variables.stat_observed_heterozygosity_spec": [[131, "sgkit-variables-stat-observed-heterozygosity-spec"]], "sgkit.variables.stat_pbs_spec": [[132, "sgkit-variables-stat-pbs-spec"]], "sgkit.variables.stat_pedigree_contribution_spec": [[133, "sgkit-variables-stat-pedigree-contribution-spec"]], "sgkit.variables.stat_pedigree_inbreeding_spec": [[134, "sgkit-variables-stat-pedigree-inbreeding-spec"]], "sgkit.variables.stat_pedigree_inverse_kinship_spec": [[135, "sgkit-variables-stat-pedigree-inverse-kinship-spec"]], "sgkit.variables.stat_pedigree_inverse_relationship_spec": [[136, "sgkit-variables-stat-pedigree-inverse-relationship-spec"]], "sgkit.variables.stat_pedigree_kinship_spec": [[137, "sgkit-variables-stat-pedigree-kinship-spec"]], "sgkit.variables.stat_pedigree_relationship_spec": [[138, "sgkit-variables-stat-pedigree-relationship-spec"]], "sgkit.variables.traits_spec": [[139, "sgkit-variables-traits-spec"]], "sgkit.variables.variant_allele_count_spec": [[140, "sgkit-variables-variant-allele-count-spec"]], "sgkit.variables.variant_allele_frequency_spec": [[141, "sgkit-variables-variant-allele-frequency-spec"]], "sgkit.variables.variant_allele_spec": [[142, "sgkit-variables-variant-allele-spec"]], "sgkit.variables.variant_allele_total_spec": [[143, "sgkit-variables-variant-allele-total-spec"]], "sgkit.variables.variant_call_rate_spec": [[144, "sgkit-variables-variant-call-rate-spec"]], "sgkit.variables.variant_contig_spec": [[145, "sgkit-variables-variant-contig-spec"]], "sgkit.variables.variant_genotype_count_spec": [[146, "sgkit-variables-variant-genotype-count-spec"]], "sgkit.variables.variant_hwe_p_value_spec": [[147, "sgkit-variables-variant-hwe-p-value-spec"]], "sgkit.variables.variant_id_spec": [[148, "sgkit-variables-variant-id-spec"]], "sgkit.variables.variant_linreg_beta_spec": [[149, "sgkit-variables-variant-linreg-beta-spec"]], "sgkit.variables.variant_linreg_p_value_spec": [[150, "sgkit-variables-variant-linreg-p-value-spec"]], "sgkit.variables.variant_linreg_t_value_spec": [[151, "sgkit-variables-variant-linreg-t-value-spec"]], "sgkit.variables.variant_n_called_spec": [[152, "sgkit-variables-variant-n-called-spec"]], "sgkit.variables.variant_n_het_spec": [[153, "sgkit-variables-variant-n-het-spec"]], "sgkit.variables.variant_n_hom_alt_spec": [[154, "sgkit-variables-variant-n-hom-alt-spec"]], "sgkit.variables.variant_n_hom_ref_spec": [[155, "sgkit-variables-variant-n-hom-ref-spec"]], "sgkit.variables.variant_n_non_ref_spec": [[156, "sgkit-variables-variant-n-non-ref-spec"]], "sgkit.variables.variant_ploidy_spec": [[157, "sgkit-variables-variant-ploidy-spec"]], "sgkit.variables.variant_position_spec": [[158, "sgkit-variables-variant-position-spec"]], "sgkit.variables.variant_score_spec": [[159, "sgkit-variables-variant-score-spec"]], "sgkit.variables.window_contig_spec": [[160, "sgkit-variables-window-contig-spec"]], "sgkit.variables.window_start_spec": [[161, "sgkit-variables-window-start-spec"]], "sgkit.variables.window_stop_spec": [[162, "sgkit-variables-window-stop-spec"]], "sgkit.variant_stats": [[163, "sgkit-variant-stats"]], "sgkit.window_by_genome": [[164, "sgkit-window-by-genome"]], "sgkit.window_by_interval": [[165, "sgkit-window-by-interval"]], "sgkit.window_by_position": [[166, "sgkit-window-by-position"]], "sgkit.window_by_variant": [[167, "sgkit-window-by-variant"]], "Getting Started": [[168, "getting-started"]], "Installation": [[168, "installation"], [173, "installation"], [174, "installation"]], "Overview": [[168, "overview"]], "Data structures": [[168, "data-structures"]], "Genetic methods": [[168, "genetic-methods"]], "Missing data": [[168, "missing-data"]], "Windowing": [[168, "windowing"]], "Cohorts": [[168, "cohorts"]], "Chaining operations": [[168, "chaining-operations"]], "Chunked arrays": [[168, "chunked-arrays"]], "How do I \u2026": [[169, "how-do-i"]], "Create a test dataset?": [[169, "create-a-test-dataset"]], "Look at the dataset summary?": [[169, "look-at-the-dataset-summary"]], "Get the values for a variable in a dataset?": [[169, "get-the-values-for-a-variable-in-a-dataset"]], "Find the definition for a variable in a dataset?": [[169, "find-the-definition-for-a-variable-in-a-dataset"]], "Look at the genotypes?": [[169, "look-at-the-genotypes"]], "Subset the variables?": [[169, "subset-the-variables"]], "Subset to a genomic range?": [[169, "subset-to-a-genomic-range"]], "Get the list of samples?": [[169, "get-the-list-of-samples"]], "Subset the samples?": [[169, "subset-the-samples"]], "Define a new variable based on others?": [[169, "define-a-new-variable-based-on-others"]], "Get summary stats?": [[169, "get-summary-stats"]], "Filter variants?": [[169, "filter-variants"]], "Find which new variables were added by a method?": [[169, "find-which-new-variables-were-added-by-a-method"]], "Save results to a Zarr file?": [[169, "save-results-to-a-zarr-file"]], "Load a dataset from Zarr?": [[169, "load-a-dataset-from-zarr"]], "sgkit: Statistical genetics toolkit in Python": [[170, "sgkit-statistical-genetics-toolkit-in-python"]], "Contents": [[170, null]], "Indices and tables": [[170, "indices-and-tables"]], "News": [[171, "news"]], "Introducing sgkit": [[172, "introducing-sgkit"]], "User Guide": [[173, "user-guide"]], "Reading and writing genetic data": [[173, "reading-and-writing-genetic-data"]], "Converting genetic data to Zarr": [[173, "converting-genetic-data-to-zarr"]], "VCF": [[173, "vcf"]], "Working with cloud-native data": [[173, "working-with-cloud-native-data"]], "Datasets": [[173, "datasets"]], "Genetic variables": [[173, "genetic-variables"]], "Dataset merge behavior": [[173, "dataset-merge-behavior"]], "Interop with other Python libraries": [[173, "interop-with-other-python-libraries"]], "Custom naming conventions": [[173, "custom-naming-conventions"]], "Adding custom data to a Dataset": [[173, "adding-custom-data-to-a-dataset"]], "Custom Computations": [[173, "custom-computations"]], "PCA": [[173, "pca"]], "Deployment": [[173, "deployment"]], "Deploying sgkit on a cluster": [[173, "deploying-sgkit-on-a-cluster"]], "Using GPUs": [[173, "using-gpus"]], "Troubleshooting": [[173, "troubleshooting"]], "Monitoring operations": [[173, "monitoring-operations"]], "Visualizing computations": [[173, "visualizing-computations"]], "Disabling the Numba cache": [[173, "disabling-the-numba-cache"]], "Reading VCF": [[174, "reading-vcf"]], "Highlights": [[174, "highlights"]], "Usage": [[174, "usage"]], "Multiple files": [[174, "multiple-files"]], "Partitioning": [[174, "partitioning"]], "Chunk sizes": [[174, "chunk-sizes"]], "Cloud storage": [[174, "cloud-storage"]], "Compression": [[174, "compression"]], "Low-level operation": [[174, "low-level-operation"]], "Polyploid and mixed-ploidy VCF": [[174, "polyploid-and-mixed-ploidy-vcf"]], "Example: converting 1000 genomes VCF to Zarr": [[174, "example-converting-1000-genomes-vcf-to-zarr"]], "Install sgkit": [[174, "install-sgkit"]], "Download the data": [[174, "download-the-data"]], "Run the conversion": [[174, "run-the-conversion"]], "Inspect the dataset": [[174, "inspect-the-dataset"]]}, "indexentries": {"fst() (in module sgkit)": [[7, "sgkit.Fst"]], "garud_h() (in module sgkit)": [[8, "sgkit.Garud_H"]], "tajimas_d() (in module sgkit)": [[9, "sgkit.Tajimas_D"]], "weir_goudet_beta() (in module sgkit)": [[10, "sgkit.Weir_Goudet_beta"]], "call_allele_frequencies() (in module sgkit)": [[11, "sgkit.call_allele_frequencies"]], "cohort_allele_frequencies() (in module sgkit)": [[12, "sgkit.cohort_allele_frequencies"]], "convert_call_to_index() (in module sgkit)": [[13, "sgkit.convert_call_to_index"]], "convert_probability_to_call() (in module sgkit)": [[14, "sgkit.convert_probability_to_call"]], "count_call_alleles() (in module sgkit)": [[15, "sgkit.count_call_alleles"]], "count_cohort_alleles() (in module sgkit)": [[16, "sgkit.count_cohort_alleles"]], "count_variant_alleles() (in module sgkit)": [[17, "sgkit.count_variant_alleles"]], "count_variant_genotypes() (in module sgkit)": [[18, "sgkit.count_variant_genotypes"]], "display_genotypes() (in module sgkit)": [[19, "sgkit.display_genotypes"]], "display_pedigree() (in module sgkit)": [[20, "sgkit.display_pedigree"]], "divergence() (in module sgkit)": [[21, "sgkit.divergence"]], "diversity() (in module sgkit)": [[22, "sgkit.diversity"]], "filter_partial_calls() (in module sgkit)": [[23, "sgkit.filter_partial_calls"]], "genee() (in module sgkit)": [[24, "sgkit.genee"]], "genomic_relationship() (in module sgkit)": [[25, "sgkit.genomic_relationship"]], "gwas_linear_regression() (in module sgkit)": [[26, "sgkit.gwas_linear_regression"]], "hardy_weinberg_test() (in module sgkit)": [[27, "sgkit.hardy_weinberg_test"]], "hybrid_inverse_relationship() (in module sgkit)": [[28, "sgkit.hybrid_inverse_relationship"]], "hybrid_relationship() (in module sgkit)": [[29, "sgkit.hybrid_relationship"]], "identity_by_state() (in module sgkit)": [[30, "sgkit.identity_by_state"]], "individual_heterozygosity() (in module sgkit)": [[31, "sgkit.individual_heterozygosity"]], "infer_call_ploidy() (in module sgkit)": [[32, "sgkit.infer_call_ploidy"]], "infer_sample_ploidy() (in module sgkit)": [[33, "sgkit.infer_sample_ploidy"]], "infer_variant_ploidy() (in module sgkit)": [[34, "sgkit.infer_variant_ploidy"]], "invert_relationship_matrix() (in module sgkit)": [[35, "sgkit.invert_relationship_matrix"]], "bgen_to_zarr() (in module sgkit.io.bgen)": [[36, "sgkit.io.bgen.bgen_to_zarr"]], "read_bgen() (in module sgkit.io.bgen)": [[37, "sgkit.io.bgen.read_bgen"]], "rechunk_bgen() (in module sgkit.io.bgen)": [[38, "sgkit.io.bgen.rechunk_bgen"]], "plink_to_zarr() (in module sgkit.io.plink)": [[39, "sgkit.io.plink.plink_to_zarr"]], "read_plink() (in module sgkit.io.plink)": [[40, "sgkit.io.plink.read_plink"]], "write_plink() (in module sgkit.io.plink)": [[41, "sgkit.io.plink.write_plink"]], "zarr_to_plink() (in module sgkit.io.plink)": [[42, "sgkit.io.plink.zarr_to_plink"]], "concat_zarrs() (in module sgkit.io.vcf)": [[43, "sgkit.io.vcf.concat_zarrs"]], "partition_into_regions() (in module sgkit.io.vcf)": [[44, "sgkit.io.vcf.partition_into_regions"]], "read_vcf() (in module sgkit.io.vcf)": [[45, "sgkit.io.vcf.read_vcf"]], "vcf_to_zarr() (in module sgkit.io.vcf)": [[46, "sgkit.io.vcf.vcf_to_zarr"]], "vcf_to_zarrs() (in module sgkit.io.vcf)": [[47, "sgkit.io.vcf.vcf_to_zarrs"]], "write_vcf() (in module sgkit.io.vcf)": [[48, "sgkit.io.vcf.write_vcf"]], "zarr_array_sizes() (in module sgkit.io.vcf)": [[49, "sgkit.io.vcf.zarr_array_sizes"]], "zarr_to_vcf() (in module sgkit.io.vcf)": [[50, "sgkit.io.vcf.zarr_to_vcf"]], "ld_matrix() (in module sgkit)": [[51, "sgkit.ld_matrix"]], "ld_prune() (in module sgkit)": [[52, "sgkit.ld_prune"]], "load_dataset() (in module sgkit)": [[53, "sgkit.load_dataset"]], "maximal_independent_set() (in module sgkit)": [[54, "sgkit.maximal_independent_set"]], "observed_heterozygosity() (in module sgkit)": [[55, "sgkit.observed_heterozygosity"]], "pairwise_distance() (in module sgkit)": [[56, "sgkit.pairwise_distance"]], "parent_indices() (in module sgkit)": [[57, "sgkit.parent_indices"]], "pbs() (in module sgkit)": [[58, "sgkit.pbs"]], "pc_relate() (in module sgkit)": [[59, "sgkit.pc_relate"]], "pedigree_contribution() (in module sgkit)": [[60, "sgkit.pedigree_contribution"]], "pedigree_inbreeding() (in module sgkit)": [[61, "sgkit.pedigree_inbreeding"]], "pedigree_inverse_kinship() (in module sgkit)": [[62, "sgkit.pedigree_inverse_kinship"]], "pedigree_kinship() (in module sgkit)": [[63, "sgkit.pedigree_kinship"]], "pedigree_sel() (in module sgkit)": [[64, "sgkit.pedigree_sel"]], "read_scikit_allel_vcfzarr() (in module sgkit)": [[65, "sgkit.read_scikit_allel_vcfzarr"]], "regenie() (in module sgkit)": [[66, "sgkit.regenie"]], "sample_stats() (in module sgkit)": [[67, "sgkit.sample_stats"]], "save_dataset() (in module sgkit)": [[68, "sgkit.save_dataset"]], "simulate_genedrop() (in module sgkit)": [[69, "sgkit.simulate_genedrop"]], "simulate_genotype_call_dataset() (in module sgkit)": [[70, "sgkit.simulate_genotype_call_dataset"]], "call_allele_count_spec (in module sgkit.variables)": [[71, "sgkit.variables.call_allele_count_spec"]], "call_allele_frequency_spec (in module sgkit.variables)": [[72, "sgkit.variables.call_allele_frequency_spec"]], "call_dosage_mask_spec (in module sgkit.variables)": [[73, "sgkit.variables.call_dosage_mask_spec"]], "call_dosage_spec (in module sgkit.variables)": [[74, "sgkit.variables.call_dosage_spec"]], "call_genotype_complete_mask_spec (in module sgkit.variables)": [[75, "sgkit.variables.call_genotype_complete_mask_spec"]], "call_genotype_complete_spec (in module sgkit.variables)": [[76, "sgkit.variables.call_genotype_complete_spec"]], "call_genotype_fill_spec (in module sgkit.variables)": [[77, "sgkit.variables.call_genotype_fill_spec"]], "call_genotype_index_mask_spec (in module sgkit.variables)": [[78, "sgkit.variables.call_genotype_index_mask_spec"]], "call_genotype_index_spec (in module sgkit.variables)": [[79, "sgkit.variables.call_genotype_index_spec"]], "call_genotype_mask_spec (in module sgkit.variables)": [[80, "sgkit.variables.call_genotype_mask_spec"]], "call_genotype_phased_spec (in module sgkit.variables)": [[81, "sgkit.variables.call_genotype_phased_spec"]], "call_genotype_probability_mask_spec (in module sgkit.variables)": [[82, "sgkit.variables.call_genotype_probability_mask_spec"]], "call_genotype_probability_spec (in module sgkit.variables)": [[83, "sgkit.variables.call_genotype_probability_spec"]], "call_genotype_spec (in module sgkit.variables)": [[84, "sgkit.variables.call_genotype_spec"]], "call_heterozygosity_spec (in module sgkit.variables)": [[85, "sgkit.variables.call_heterozygosity_spec"]], "call_ploidy_spec (in module sgkit.variables)": [[86, "sgkit.variables.call_ploidy_spec"]], "cohort_allele_count_spec (in module sgkit.variables)": [[87, "sgkit.variables.cohort_allele_count_spec"]], "cohort_allele_frequency_spec (in module sgkit.variables)": [[88, "sgkit.variables.cohort_allele_frequency_spec"]], "covariates_spec (in module sgkit.variables)": [[89, "sgkit.variables.covariates_spec"]], "interval_contig_name_spec (in module sgkit.variables)": [[90, "sgkit.variables.interval_contig_name_spec"]], "interval_start_spec (in module sgkit.variables)": [[91, "sgkit.variables.interval_start_spec"]], "interval_stop_spec (in module sgkit.variables)": [[92, "sgkit.variables.interval_stop_spec"]], "ld_prune_index_to_drop_spec (in module sgkit.variables)": [[93, "sgkit.variables.ld_prune_index_to_drop_spec"]], "parent_id_spec (in module sgkit.variables)": [[94, "sgkit.variables.parent_id_spec"]], "parent_spec (in module sgkit.variables)": [[95, "sgkit.variables.parent_spec"]], "pc_relate_phi_spec (in module sgkit.variables)": [[96, "sgkit.variables.pc_relate_phi_spec"]], "regenie_base_prediction_spec (in module sgkit.variables)": [[97, "sgkit.variables.regenie_base_prediction_spec"]], "regenie_loco_prediction_spec (in module sgkit.variables)": [[98, "sgkit.variables.regenie_loco_prediction_spec"]], "regenie_meta_prediction_spec (in module sgkit.variables)": [[99, "sgkit.variables.regenie_meta_prediction_spec"]], "sample_call_rate_spec (in module sgkit.variables)": [[100, "sgkit.variables.sample_call_rate_spec"]], "sample_cohort_spec (in module sgkit.variables)": [[101, "sgkit.variables.sample_cohort_spec"]], "sample_id_spec (in module sgkit.variables)": [[102, "sgkit.variables.sample_id_spec"]], "sample_n_called_spec (in module sgkit.variables)": [[103, "sgkit.variables.sample_n_called_spec"]], "sample_n_het_spec (in module sgkit.variables)": [[104, "sgkit.variables.sample_n_het_spec"]], "sample_n_hom_alt_spec (in module sgkit.variables)": [[105, "sgkit.variables.sample_n_hom_alt_spec"]], "sample_n_hom_ref_spec (in module sgkit.variables)": [[106, "sgkit.variables.sample_n_hom_ref_spec"]], "sample_n_non_ref_spec (in module sgkit.variables)": [[107, "sgkit.variables.sample_n_non_ref_spec"]], "sample_pca_component_spec (in module sgkit.variables)": [[108, "sgkit.variables.sample_pca_component_spec"]], "sample_pca_explained_variance_ratio_spec (in module sgkit.variables)": [[109, "sgkit.variables.sample_pca_explained_variance_ratio_spec"]], "sample_pca_explained_variance_spec (in module sgkit.variables)": [[110, "sgkit.variables.sample_pca_explained_variance_spec"]], "sample_pca_loading_spec (in module sgkit.variables)": [[111, "sgkit.variables.sample_pca_loading_spec"]], "sample_pca_projection_spec (in module sgkit.variables)": [[112, "sgkit.variables.sample_pca_projection_spec"]], "sample_ploidy_spec (in module sgkit.variables)": [[113, "sgkit.variables.sample_ploidy_spec"]], "stat_fst_spec (in module sgkit.variables)": [[114, "sgkit.variables.stat_Fst_spec"]], "stat_garud_h123_spec (in module sgkit.variables)": [[115, "sgkit.variables.stat_Garud_h123_spec"]], "stat_garud_h12_spec (in module sgkit.variables)": [[116, "sgkit.variables.stat_Garud_h12_spec"]], "stat_garud_h1_spec (in module sgkit.variables)": [[117, "sgkit.variables.stat_Garud_h1_spec"]], "stat_garud_h2_h1_spec (in module sgkit.variables)": [[118, "sgkit.variables.stat_Garud_h2_h1_spec"]], "stat_hamilton_kerr_lambda_spec (in module sgkit.variables)": [[119, "sgkit.variables.stat_Hamilton_Kerr_lambda_spec"]], "stat_hamilton_kerr_tau_spec (in module sgkit.variables)": [[120, "sgkit.variables.stat_Hamilton_Kerr_tau_spec"]], "stat_tajimas_d_spec (in module sgkit.variables)": [[121, "sgkit.variables.stat_Tajimas_D_spec"]], "stat_weir_goudet_beta_spec (in module sgkit.variables)": [[122, "sgkit.variables.stat_Weir_Goudet_beta_spec"]], "stat_divergence_spec (in module sgkit.variables)": [[123, "sgkit.variables.stat_divergence_spec"]], "stat_diversity_spec (in module sgkit.variables)": [[124, "sgkit.variables.stat_diversity_spec"]], "stat_genomic_kinship_spec (in module sgkit.variables)": [[125, "sgkit.variables.stat_genomic_kinship_spec"]], "stat_genomic_relationship_spec (in module sgkit.variables)": [[126, "sgkit.variables.stat_genomic_relationship_spec"]], "stat_hybrid_inverse_relationship_spec (in module sgkit.variables)": [[127, "sgkit.variables.stat_hybrid_inverse_relationship_spec"]], "stat_hybrid_relationship_spec (in module sgkit.variables)": [[128, "sgkit.variables.stat_hybrid_relationship_spec"]], "stat_identity_by_state_spec (in module sgkit.variables)": [[129, "sgkit.variables.stat_identity_by_state_spec"]], "stat_inverse_relationship_spec (in module sgkit.variables)": [[130, "sgkit.variables.stat_inverse_relationship_spec"]], "stat_observed_heterozygosity_spec (in module sgkit.variables)": [[131, "sgkit.variables.stat_observed_heterozygosity_spec"]], "stat_pbs_spec (in module sgkit.variables)": [[132, "sgkit.variables.stat_pbs_spec"]], "stat_pedigree_contribution_spec (in module sgkit.variables)": [[133, "sgkit.variables.stat_pedigree_contribution_spec"]], "stat_pedigree_inbreeding_spec (in module sgkit.variables)": [[134, "sgkit.variables.stat_pedigree_inbreeding_spec"]], "stat_pedigree_inverse_kinship_spec (in module sgkit.variables)": [[135, "sgkit.variables.stat_pedigree_inverse_kinship_spec"]], "stat_pedigree_inverse_relationship_spec (in module sgkit.variables)": [[136, "sgkit.variables.stat_pedigree_inverse_relationship_spec"]], "stat_pedigree_kinship_spec (in module sgkit.variables)": [[137, "sgkit.variables.stat_pedigree_kinship_spec"]], "stat_pedigree_relationship_spec (in module sgkit.variables)": [[138, "sgkit.variables.stat_pedigree_relationship_spec"]], "traits_spec (in module sgkit.variables)": [[139, "sgkit.variables.traits_spec"]], "variant_allele_count_spec (in module sgkit.variables)": [[140, "sgkit.variables.variant_allele_count_spec"]], "variant_allele_frequency_spec (in module sgkit.variables)": [[141, "sgkit.variables.variant_allele_frequency_spec"]], "variant_allele_spec (in module sgkit.variables)": [[142, "sgkit.variables.variant_allele_spec"]], "variant_allele_total_spec (in module sgkit.variables)": [[143, "sgkit.variables.variant_allele_total_spec"]], "variant_call_rate_spec (in module sgkit.variables)": [[144, "sgkit.variables.variant_call_rate_spec"]], "variant_contig_spec (in module sgkit.variables)": [[145, "sgkit.variables.variant_contig_spec"]], "variant_genotype_count_spec (in module sgkit.variables)": [[146, "sgkit.variables.variant_genotype_count_spec"]], "variant_hwe_p_value_spec (in module sgkit.variables)": [[147, "sgkit.variables.variant_hwe_p_value_spec"]], "variant_id_spec (in module sgkit.variables)": [[148, "sgkit.variables.variant_id_spec"]], "variant_linreg_beta_spec (in module sgkit.variables)": [[149, "sgkit.variables.variant_linreg_beta_spec"]], "variant_linreg_p_value_spec (in module sgkit.variables)": [[150, "sgkit.variables.variant_linreg_p_value_spec"]], "variant_linreg_t_value_spec (in module sgkit.variables)": [[151, "sgkit.variables.variant_linreg_t_value_spec"]], "variant_n_called_spec (in module sgkit.variables)": [[152, "sgkit.variables.variant_n_called_spec"]], "variant_n_het_spec (in module sgkit.variables)": [[153, "sgkit.variables.variant_n_het_spec"]], "variant_n_hom_alt_spec (in module sgkit.variables)": [[154, "sgkit.variables.variant_n_hom_alt_spec"]], "variant_n_hom_ref_spec (in module sgkit.variables)": [[155, "sgkit.variables.variant_n_hom_ref_spec"]], "variant_n_non_ref_spec (in module sgkit.variables)": [[156, "sgkit.variables.variant_n_non_ref_spec"]], "variant_ploidy_spec (in module sgkit.variables)": [[157, "sgkit.variables.variant_ploidy_spec"]], "variant_position_spec (in module sgkit.variables)": [[158, "sgkit.variables.variant_position_spec"]], "variant_score_spec (in module sgkit.variables)": [[159, "sgkit.variables.variant_score_spec"]], "window_contig_spec (in module sgkit.variables)": [[160, "sgkit.variables.window_contig_spec"]], "window_start_spec (in module sgkit.variables)": [[161, "sgkit.variables.window_start_spec"]], "window_stop_spec (in module sgkit.variables)": [[162, "sgkit.variables.window_stop_spec"]], "variant_stats() (in module sgkit)": [[163, "sgkit.variant_stats"]], "window_by_genome() (in module sgkit)": [[164, "sgkit.window_by_genome"]], "window_by_interval() (in module sgkit)": [[165, "sgkit.window_by_interval"]], "window_by_position() (in module sgkit)": [[166, "sgkit.window_by_position"]], "window_by_variant() (in module sgkit)": [[167, "sgkit.window_by_variant"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["about", "api", "changelog", "contributing", "examples/gwas_tutorial", "examples/index", "examples/relatedness_tutorial", "generated/sgkit.Fst", "generated/sgkit.Garud_H", "generated/sgkit.Tajimas_D", "generated/sgkit.Weir_Goudet_beta", "generated/sgkit.call_allele_frequencies", "generated/sgkit.cohort_allele_frequencies", "generated/sgkit.convert_call_to_index", "generated/sgkit.convert_probability_to_call", "generated/sgkit.count_call_alleles", "generated/sgkit.count_cohort_alleles", "generated/sgkit.count_variant_alleles", "generated/sgkit.count_variant_genotypes", "generated/sgkit.display_genotypes", "generated/sgkit.display_pedigree", "generated/sgkit.divergence", "generated/sgkit.diversity", "generated/sgkit.filter_partial_calls", "generated/sgkit.genee", "generated/sgkit.genomic_relationship", "generated/sgkit.gwas_linear_regression", "generated/sgkit.hardy_weinberg_test", "generated/sgkit.hybrid_inverse_relationship", "generated/sgkit.hybrid_relationship", "generated/sgkit.identity_by_state", "generated/sgkit.individual_heterozygosity", "generated/sgkit.infer_call_ploidy", "generated/sgkit.infer_sample_ploidy", "generated/sgkit.infer_variant_ploidy", "generated/sgkit.invert_relationship_matrix", "generated/sgkit.io.bgen.bgen_to_zarr", "generated/sgkit.io.bgen.read_bgen", "generated/sgkit.io.bgen.rechunk_bgen", "generated/sgkit.io.plink.plink_to_zarr", "generated/sgkit.io.plink.read_plink", "generated/sgkit.io.plink.write_plink", "generated/sgkit.io.plink.zarr_to_plink", "generated/sgkit.io.vcf.concat_zarrs", "generated/sgkit.io.vcf.partition_into_regions", "generated/sgkit.io.vcf.read_vcf", "generated/sgkit.io.vcf.vcf_to_zarr", "generated/sgkit.io.vcf.vcf_to_zarrs", "generated/sgkit.io.vcf.write_vcf", "generated/sgkit.io.vcf.zarr_array_sizes", "generated/sgkit.io.vcf.zarr_to_vcf", "generated/sgkit.ld_matrix", "generated/sgkit.ld_prune", "generated/sgkit.load_dataset", "generated/sgkit.maximal_independent_set", "generated/sgkit.observed_heterozygosity", "generated/sgkit.pairwise_distance", "generated/sgkit.parent_indices", "generated/sgkit.pbs", "generated/sgkit.pc_relate", "generated/sgkit.pedigree_contribution", "generated/sgkit.pedigree_inbreeding", "generated/sgkit.pedigree_inverse_kinship", "generated/sgkit.pedigree_kinship", "generated/sgkit.pedigree_sel", "generated/sgkit.read_scikit_allel_vcfzarr", "generated/sgkit.regenie", "generated/sgkit.sample_stats", "generated/sgkit.save_dataset", "generated/sgkit.simulate_genedrop", "generated/sgkit.simulate_genotype_call_dataset", "generated/sgkit.variables.call_allele_count_spec", "generated/sgkit.variables.call_allele_frequency_spec", "generated/sgkit.variables.call_dosage_mask_spec", "generated/sgkit.variables.call_dosage_spec", "generated/sgkit.variables.call_genotype_complete_mask_spec", "generated/sgkit.variables.call_genotype_complete_spec", "generated/sgkit.variables.call_genotype_fill_spec", "generated/sgkit.variables.call_genotype_index_mask_spec", "generated/sgkit.variables.call_genotype_index_spec", "generated/sgkit.variables.call_genotype_mask_spec", "generated/sgkit.variables.call_genotype_phased_spec", "generated/sgkit.variables.call_genotype_probability_mask_spec", "generated/sgkit.variables.call_genotype_probability_spec", "generated/sgkit.variables.call_genotype_spec", "generated/sgkit.variables.call_heterozygosity_spec", "generated/sgkit.variables.call_ploidy_spec", "generated/sgkit.variables.cohort_allele_count_spec", "generated/sgkit.variables.cohort_allele_frequency_spec", "generated/sgkit.variables.covariates_spec", "generated/sgkit.variables.interval_contig_name_spec", "generated/sgkit.variables.interval_start_spec", "generated/sgkit.variables.interval_stop_spec", "generated/sgkit.variables.ld_prune_index_to_drop_spec", "generated/sgkit.variables.parent_id_spec", "generated/sgkit.variables.parent_spec", "generated/sgkit.variables.pc_relate_phi_spec", "generated/sgkit.variables.regenie_base_prediction_spec", "generated/sgkit.variables.regenie_loco_prediction_spec", "generated/sgkit.variables.regenie_meta_prediction_spec", "generated/sgkit.variables.sample_call_rate_spec", "generated/sgkit.variables.sample_cohort_spec", "generated/sgkit.variables.sample_id_spec", "generated/sgkit.variables.sample_n_called_spec", "generated/sgkit.variables.sample_n_het_spec", "generated/sgkit.variables.sample_n_hom_alt_spec", "generated/sgkit.variables.sample_n_hom_ref_spec", "generated/sgkit.variables.sample_n_non_ref_spec", "generated/sgkit.variables.sample_pca_component_spec", "generated/sgkit.variables.sample_pca_explained_variance_ratio_spec", "generated/sgkit.variables.sample_pca_explained_variance_spec", "generated/sgkit.variables.sample_pca_loading_spec", "generated/sgkit.variables.sample_pca_projection_spec", "generated/sgkit.variables.sample_ploidy_spec", "generated/sgkit.variables.stat_Fst_spec", "generated/sgkit.variables.stat_Garud_h123_spec", "generated/sgkit.variables.stat_Garud_h12_spec", "generated/sgkit.variables.stat_Garud_h1_spec", "generated/sgkit.variables.stat_Garud_h2_h1_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec", "generated/sgkit.variables.stat_Tajimas_D_spec", "generated/sgkit.variables.stat_Weir_Goudet_beta_spec", "generated/sgkit.variables.stat_divergence_spec", "generated/sgkit.variables.stat_diversity_spec", "generated/sgkit.variables.stat_genomic_kinship_spec", "generated/sgkit.variables.stat_genomic_relationship_spec", "generated/sgkit.variables.stat_hybrid_inverse_relationship_spec", "generated/sgkit.variables.stat_hybrid_relationship_spec", "generated/sgkit.variables.stat_identity_by_state_spec", "generated/sgkit.variables.stat_inverse_relationship_spec", "generated/sgkit.variables.stat_observed_heterozygosity_spec", "generated/sgkit.variables.stat_pbs_spec", "generated/sgkit.variables.stat_pedigree_contribution_spec", "generated/sgkit.variables.stat_pedigree_inbreeding_spec", "generated/sgkit.variables.stat_pedigree_inverse_kinship_spec", "generated/sgkit.variables.stat_pedigree_inverse_relationship_spec", "generated/sgkit.variables.stat_pedigree_kinship_spec", "generated/sgkit.variables.stat_pedigree_relationship_spec", "generated/sgkit.variables.traits_spec", "generated/sgkit.variables.variant_allele_count_spec", "generated/sgkit.variables.variant_allele_frequency_spec", "generated/sgkit.variables.variant_allele_spec", "generated/sgkit.variables.variant_allele_total_spec", "generated/sgkit.variables.variant_call_rate_spec", "generated/sgkit.variables.variant_contig_spec", "generated/sgkit.variables.variant_genotype_count_spec", "generated/sgkit.variables.variant_hwe_p_value_spec", "generated/sgkit.variables.variant_id_spec", "generated/sgkit.variables.variant_linreg_beta_spec", "generated/sgkit.variables.variant_linreg_p_value_spec", "generated/sgkit.variables.variant_linreg_t_value_spec", "generated/sgkit.variables.variant_n_called_spec", "generated/sgkit.variables.variant_n_het_spec", "generated/sgkit.variables.variant_n_hom_alt_spec", "generated/sgkit.variables.variant_n_hom_ref_spec", "generated/sgkit.variables.variant_n_non_ref_spec", "generated/sgkit.variables.variant_ploidy_spec", "generated/sgkit.variables.variant_position_spec", "generated/sgkit.variables.variant_score_spec", "generated/sgkit.variables.window_contig_spec", "generated/sgkit.variables.window_start_spec", "generated/sgkit.variables.window_stop_spec", "generated/sgkit.variant_stats", "generated/sgkit.window_by_genome", "generated/sgkit.window_by_interval", "generated/sgkit.window_by_position", "generated/sgkit.window_by_variant", "getting_started", "how_do_i", "index", "news", "news/introducing_sgkit", "user_guide", "vcf"], "filenames": ["about.rst", "api.rst", "changelog.rst", "contributing.rst", "examples/gwas_tutorial.ipynb", "examples/index.rst", "examples/relatedness_tutorial.ipynb", "generated/sgkit.Fst.rst", "generated/sgkit.Garud_H.rst", "generated/sgkit.Tajimas_D.rst", "generated/sgkit.Weir_Goudet_beta.rst", "generated/sgkit.call_allele_frequencies.rst", "generated/sgkit.cohort_allele_frequencies.rst", "generated/sgkit.convert_call_to_index.rst", "generated/sgkit.convert_probability_to_call.rst", "generated/sgkit.count_call_alleles.rst", "generated/sgkit.count_cohort_alleles.rst", "generated/sgkit.count_variant_alleles.rst", "generated/sgkit.count_variant_genotypes.rst", "generated/sgkit.display_genotypes.rst", "generated/sgkit.display_pedigree.rst", "generated/sgkit.divergence.rst", "generated/sgkit.diversity.rst", "generated/sgkit.filter_partial_calls.rst", "generated/sgkit.genee.rst", "generated/sgkit.genomic_relationship.rst", "generated/sgkit.gwas_linear_regression.rst", "generated/sgkit.hardy_weinberg_test.rst", "generated/sgkit.hybrid_inverse_relationship.rst", "generated/sgkit.hybrid_relationship.rst", "generated/sgkit.identity_by_state.rst", "generated/sgkit.individual_heterozygosity.rst", "generated/sgkit.infer_call_ploidy.rst", "generated/sgkit.infer_sample_ploidy.rst", "generated/sgkit.infer_variant_ploidy.rst", "generated/sgkit.invert_relationship_matrix.rst", "generated/sgkit.io.bgen.bgen_to_zarr.rst", "generated/sgkit.io.bgen.read_bgen.rst", "generated/sgkit.io.bgen.rechunk_bgen.rst", "generated/sgkit.io.plink.plink_to_zarr.rst", "generated/sgkit.io.plink.read_plink.rst", "generated/sgkit.io.plink.write_plink.rst", "generated/sgkit.io.plink.zarr_to_plink.rst", "generated/sgkit.io.vcf.concat_zarrs.rst", "generated/sgkit.io.vcf.partition_into_regions.rst", "generated/sgkit.io.vcf.read_vcf.rst", "generated/sgkit.io.vcf.vcf_to_zarr.rst", "generated/sgkit.io.vcf.vcf_to_zarrs.rst", "generated/sgkit.io.vcf.write_vcf.rst", "generated/sgkit.io.vcf.zarr_array_sizes.rst", "generated/sgkit.io.vcf.zarr_to_vcf.rst", "generated/sgkit.ld_matrix.rst", "generated/sgkit.ld_prune.rst", "generated/sgkit.load_dataset.rst", "generated/sgkit.maximal_independent_set.rst", "generated/sgkit.observed_heterozygosity.rst", "generated/sgkit.pairwise_distance.rst", "generated/sgkit.parent_indices.rst", "generated/sgkit.pbs.rst", "generated/sgkit.pc_relate.rst", "generated/sgkit.pedigree_contribution.rst", "generated/sgkit.pedigree_inbreeding.rst", "generated/sgkit.pedigree_inverse_kinship.rst", "generated/sgkit.pedigree_kinship.rst", "generated/sgkit.pedigree_sel.rst", "generated/sgkit.read_scikit_allel_vcfzarr.rst", "generated/sgkit.regenie.rst", "generated/sgkit.sample_stats.rst", "generated/sgkit.save_dataset.rst", "generated/sgkit.simulate_genedrop.rst", "generated/sgkit.simulate_genotype_call_dataset.rst", "generated/sgkit.variables.call_allele_count_spec.rst", "generated/sgkit.variables.call_allele_frequency_spec.rst", "generated/sgkit.variables.call_dosage_mask_spec.rst", "generated/sgkit.variables.call_dosage_spec.rst", "generated/sgkit.variables.call_genotype_complete_mask_spec.rst", "generated/sgkit.variables.call_genotype_complete_spec.rst", "generated/sgkit.variables.call_genotype_fill_spec.rst", "generated/sgkit.variables.call_genotype_index_mask_spec.rst", "generated/sgkit.variables.call_genotype_index_spec.rst", "generated/sgkit.variables.call_genotype_mask_spec.rst", "generated/sgkit.variables.call_genotype_phased_spec.rst", "generated/sgkit.variables.call_genotype_probability_mask_spec.rst", "generated/sgkit.variables.call_genotype_probability_spec.rst", "generated/sgkit.variables.call_genotype_spec.rst", "generated/sgkit.variables.call_heterozygosity_spec.rst", "generated/sgkit.variables.call_ploidy_spec.rst", "generated/sgkit.variables.cohort_allele_count_spec.rst", "generated/sgkit.variables.cohort_allele_frequency_spec.rst", "generated/sgkit.variables.covariates_spec.rst", "generated/sgkit.variables.interval_contig_name_spec.rst", "generated/sgkit.variables.interval_start_spec.rst", "generated/sgkit.variables.interval_stop_spec.rst", "generated/sgkit.variables.ld_prune_index_to_drop_spec.rst", "generated/sgkit.variables.parent_id_spec.rst", "generated/sgkit.variables.parent_spec.rst", "generated/sgkit.variables.pc_relate_phi_spec.rst", "generated/sgkit.variables.regenie_base_prediction_spec.rst", "generated/sgkit.variables.regenie_loco_prediction_spec.rst", "generated/sgkit.variables.regenie_meta_prediction_spec.rst", "generated/sgkit.variables.sample_call_rate_spec.rst", "generated/sgkit.variables.sample_cohort_spec.rst", "generated/sgkit.variables.sample_id_spec.rst", "generated/sgkit.variables.sample_n_called_spec.rst", "generated/sgkit.variables.sample_n_het_spec.rst", "generated/sgkit.variables.sample_n_hom_alt_spec.rst", "generated/sgkit.variables.sample_n_hom_ref_spec.rst", "generated/sgkit.variables.sample_n_non_ref_spec.rst", "generated/sgkit.variables.sample_pca_component_spec.rst", "generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.rst", "generated/sgkit.variables.sample_pca_explained_variance_spec.rst", "generated/sgkit.variables.sample_pca_loading_spec.rst", "generated/sgkit.variables.sample_pca_projection_spec.rst", "generated/sgkit.variables.sample_ploidy_spec.rst", "generated/sgkit.variables.stat_Fst_spec.rst", "generated/sgkit.variables.stat_Garud_h123_spec.rst", "generated/sgkit.variables.stat_Garud_h12_spec.rst", "generated/sgkit.variables.stat_Garud_h1_spec.rst", "generated/sgkit.variables.stat_Garud_h2_h1_spec.rst", "generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.rst", "generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.rst", "generated/sgkit.variables.stat_Tajimas_D_spec.rst", "generated/sgkit.variables.stat_Weir_Goudet_beta_spec.rst", "generated/sgkit.variables.stat_divergence_spec.rst", "generated/sgkit.variables.stat_diversity_spec.rst", "generated/sgkit.variables.stat_genomic_kinship_spec.rst", "generated/sgkit.variables.stat_genomic_relationship_spec.rst", "generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_hybrid_relationship_spec.rst", "generated/sgkit.variables.stat_identity_by_state_spec.rst", "generated/sgkit.variables.stat_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_observed_heterozygosity_spec.rst", "generated/sgkit.variables.stat_pbs_spec.rst", "generated/sgkit.variables.stat_pedigree_contribution_spec.rst", "generated/sgkit.variables.stat_pedigree_inbreeding_spec.rst", "generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.rst", "generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_pedigree_kinship_spec.rst", "generated/sgkit.variables.stat_pedigree_relationship_spec.rst", "generated/sgkit.variables.traits_spec.rst", "generated/sgkit.variables.variant_allele_count_spec.rst", "generated/sgkit.variables.variant_allele_frequency_spec.rst", "generated/sgkit.variables.variant_allele_spec.rst", "generated/sgkit.variables.variant_allele_total_spec.rst", "generated/sgkit.variables.variant_call_rate_spec.rst", "generated/sgkit.variables.variant_contig_spec.rst", "generated/sgkit.variables.variant_genotype_count_spec.rst", "generated/sgkit.variables.variant_hwe_p_value_spec.rst", "generated/sgkit.variables.variant_id_spec.rst", "generated/sgkit.variables.variant_linreg_beta_spec.rst", "generated/sgkit.variables.variant_linreg_p_value_spec.rst", "generated/sgkit.variables.variant_linreg_t_value_spec.rst", "generated/sgkit.variables.variant_n_called_spec.rst", "generated/sgkit.variables.variant_n_het_spec.rst", "generated/sgkit.variables.variant_n_hom_alt_spec.rst", "generated/sgkit.variables.variant_n_hom_ref_spec.rst", "generated/sgkit.variables.variant_n_non_ref_spec.rst", "generated/sgkit.variables.variant_ploidy_spec.rst", "generated/sgkit.variables.variant_position_spec.rst", "generated/sgkit.variables.variant_score_spec.rst", "generated/sgkit.variables.window_contig_spec.rst", "generated/sgkit.variables.window_start_spec.rst", "generated/sgkit.variables.window_stop_spec.rst", "generated/sgkit.variant_stats.rst", "generated/sgkit.window_by_genome.rst", "generated/sgkit.window_by_interval.rst", "generated/sgkit.window_by_position.rst", "generated/sgkit.window_by_variant.rst", "getting_started.rst", "how_do_i.rst", "index.rst", "news.rst", "news/introducing_sgkit.md", "user_guide.rst", "vcf.rst"], "titles": ["About", "API reference", "Changelog", "Contributing to sgkit", "GWAS Tutorial", "Examples", "Relatedness Tutorial", "sgkit.Fst", "sgkit.Garud_H", "sgkit.Tajimas_D", "sgkit.Weir_Goudet_beta", "sgkit.call_allele_frequencies", "sgkit.cohort_allele_frequencies", "sgkit.convert_call_to_index", "sgkit.convert_probability_to_call", "sgkit.count_call_alleles", "sgkit.count_cohort_alleles", "sgkit.count_variant_alleles", "sgkit.count_variant_genotypes", "sgkit.display_genotypes", "sgkit.display_pedigree", "sgkit.divergence", "sgkit.diversity", "sgkit.filter_partial_calls", "sgkit.genee", "sgkit.genomic_relationship", "sgkit.gwas_linear_regression", "sgkit.hardy_weinberg_test", "sgkit.hybrid_inverse_relationship", "sgkit.hybrid_relationship", "sgkit.identity_by_state", "sgkit.individual_heterozygosity", "sgkit.infer_call_ploidy", "sgkit.infer_sample_ploidy", "sgkit.infer_variant_ploidy", "sgkit.invert_relationship_matrix", "sgkit.io.bgen.bgen_to_zarr", "sgkit.io.bgen.read_bgen", "sgkit.io.bgen.rechunk_bgen", "sgkit.io.plink.plink_to_zarr", "sgkit.io.plink.read_plink", "sgkit.io.plink.write_plink", "sgkit.io.plink.zarr_to_plink", "sgkit.io.vcf.concat_zarrs", "sgkit.io.vcf.partition_into_regions", "sgkit.io.vcf.read_vcf", "sgkit.io.vcf.vcf_to_zarr", "sgkit.io.vcf.vcf_to_zarrs", "sgkit.io.vcf.write_vcf", "sgkit.io.vcf.zarr_array_sizes", "sgkit.io.vcf.zarr_to_vcf", "sgkit.ld_matrix", "sgkit.ld_prune", "sgkit.load_dataset", "sgkit.maximal_independent_set", "sgkit.observed_heterozygosity", "sgkit.pairwise_distance", "sgkit.parent_indices", "sgkit.pbs", "sgkit.pc_relate", "sgkit.pedigree_contribution", "sgkit.pedigree_inbreeding", "sgkit.pedigree_inverse_kinship", "sgkit.pedigree_kinship", "sgkit.pedigree_sel", "sgkit.read_scikit_allel_vcfzarr", "sgkit.regenie", "sgkit.sample_stats", "sgkit.save_dataset", "sgkit.simulate_genedrop", "sgkit.simulate_genotype_call_dataset", "sgkit.variables.call_allele_count_spec", "sgkit.variables.call_allele_frequency_spec", "sgkit.variables.call_dosage_mask_spec", "sgkit.variables.call_dosage_spec", "sgkit.variables.call_genotype_complete_mask_spec", "sgkit.variables.call_genotype_complete_spec", "sgkit.variables.call_genotype_fill_spec", "sgkit.variables.call_genotype_index_mask_spec", "sgkit.variables.call_genotype_index_spec", "sgkit.variables.call_genotype_mask_spec", "sgkit.variables.call_genotype_phased_spec", "sgkit.variables.call_genotype_probability_mask_spec", "sgkit.variables.call_genotype_probability_spec", "sgkit.variables.call_genotype_spec", "sgkit.variables.call_heterozygosity_spec", "sgkit.variables.call_ploidy_spec", "sgkit.variables.cohort_allele_count_spec", "sgkit.variables.cohort_allele_frequency_spec", "sgkit.variables.covariates_spec", "sgkit.variables.interval_contig_name_spec", "sgkit.variables.interval_start_spec", "sgkit.variables.interval_stop_spec", "sgkit.variables.ld_prune_index_to_drop_spec", "sgkit.variables.parent_id_spec", "sgkit.variables.parent_spec", "sgkit.variables.pc_relate_phi_spec", "sgkit.variables.regenie_base_prediction_spec", "sgkit.variables.regenie_loco_prediction_spec", "sgkit.variables.regenie_meta_prediction_spec", "sgkit.variables.sample_call_rate_spec", "sgkit.variables.sample_cohort_spec", "sgkit.variables.sample_id_spec", "sgkit.variables.sample_n_called_spec", "sgkit.variables.sample_n_het_spec", "sgkit.variables.sample_n_hom_alt_spec", "sgkit.variables.sample_n_hom_ref_spec", "sgkit.variables.sample_n_non_ref_spec", "sgkit.variables.sample_pca_component_spec", "sgkit.variables.sample_pca_explained_variance_ratio_spec", "sgkit.variables.sample_pca_explained_variance_spec", "sgkit.variables.sample_pca_loading_spec", "sgkit.variables.sample_pca_projection_spec", "sgkit.variables.sample_ploidy_spec", "sgkit.variables.stat_Fst_spec", "sgkit.variables.stat_Garud_h123_spec", "sgkit.variables.stat_Garud_h12_spec", "sgkit.variables.stat_Garud_h1_spec", "sgkit.variables.stat_Garud_h2_h1_spec", "sgkit.variables.stat_Hamilton_Kerr_lambda_spec", "sgkit.variables.stat_Hamilton_Kerr_tau_spec", "sgkit.variables.stat_Tajimas_D_spec", "sgkit.variables.stat_Weir_Goudet_beta_spec", "sgkit.variables.stat_divergence_spec", "sgkit.variables.stat_diversity_spec", "sgkit.variables.stat_genomic_kinship_spec", "sgkit.variables.stat_genomic_relationship_spec", "sgkit.variables.stat_hybrid_inverse_relationship_spec", "sgkit.variables.stat_hybrid_relationship_spec", "sgkit.variables.stat_identity_by_state_spec", "sgkit.variables.stat_inverse_relationship_spec", "sgkit.variables.stat_observed_heterozygosity_spec", "sgkit.variables.stat_pbs_spec", "sgkit.variables.stat_pedigree_contribution_spec", "sgkit.variables.stat_pedigree_inbreeding_spec", "sgkit.variables.stat_pedigree_inverse_kinship_spec", "sgkit.variables.stat_pedigree_inverse_relationship_spec", "sgkit.variables.stat_pedigree_kinship_spec", "sgkit.variables.stat_pedigree_relationship_spec", "sgkit.variables.traits_spec", "sgkit.variables.variant_allele_count_spec", "sgkit.variables.variant_allele_frequency_spec", "sgkit.variables.variant_allele_spec", "sgkit.variables.variant_allele_total_spec", "sgkit.variables.variant_call_rate_spec", "sgkit.variables.variant_contig_spec", "sgkit.variables.variant_genotype_count_spec", "sgkit.variables.variant_hwe_p_value_spec", "sgkit.variables.variant_id_spec", "sgkit.variables.variant_linreg_beta_spec", "sgkit.variables.variant_linreg_p_value_spec", "sgkit.variables.variant_linreg_t_value_spec", "sgkit.variables.variant_n_called_spec", "sgkit.variables.variant_n_het_spec", "sgkit.variables.variant_n_hom_alt_spec", "sgkit.variables.variant_n_hom_ref_spec", "sgkit.variables.variant_n_non_ref_spec", "sgkit.variables.variant_ploidy_spec", "sgkit.variables.variant_position_spec", "sgkit.variables.variant_score_spec", "sgkit.variables.window_contig_spec", "sgkit.variables.window_start_spec", "sgkit.variables.window_stop_spec", "sgkit.variant_stats", "sgkit.window_by_genome", "sgkit.window_by_interval", "sgkit.window_by_position", "sgkit.window_by_variant", "Getting Started", "How do I \u2026", "sgkit: Statistical genetics toolkit in Python", "News", "Introducing sgkit", "User Guide", "Reading VCF"], "terms": {"sgkit": [0, 1, 2, 4, 5, 6, 168, 169, 171], "i": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 74, 76, 79, 81, 84, 86, 91, 92, 93, 95, 101, 103, 104, 105, 106, 107, 108, 109, 110, 112, 113, 133, 143, 145, 146, 152, 153, 154, 155, 156, 157, 158, 160, 161, 162, 163, 165, 166, 168, 170, 171, 172, 173, 174], "fiscal": 0, "sponsor": [0, 172], "project": [0, 3, 6, 26, 112, 172, 173], "numfocu": [0, 172], "nonprofit": 0, "dedic": 0, "support": [0, 2, 3, 6, 7, 9, 13, 18, 21, 22, 25, 27, 37, 40, 48, 58, 60, 66, 67, 163, 171, 172, 173, 174], "open": [0, 4, 6, 39, 40, 43, 44, 45, 46, 47, 53, 68, 173], "sourc": [0, 3, 4, 168, 169, 173], "scientif": [0, 48], "comput": [0, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 51, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 69, 74, 163, 164, 165, 166, 167, 168, 169, 174], "commun": [0, 3], "If": [0, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 50, 51, 52, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 81, 163, 164, 165, 166, 167, 168, 172, 173, 174], "you": [0, 3, 4, 6, 40, 168, 169, 172, 173, 174], "like": [0, 3, 4, 6, 26, 27, 56, 165, 168, 169, 173, 174], "want": [0, 4, 6, 168, 169, 174], "our": [0, 3, 6, 168, 172, 173], "mission": 0, "pleas": [0, 1, 3, 6, 40, 43, 44, 45, 46, 47, 49, 65, 169, 171, 172, 173, 174], "consid": [0, 2, 46, 52, 56, 174], "make": [0, 3, 4, 6, 37, 49, 53, 68, 168, 169, 170, 173, 174], "donat": 0, "effort": 0, "501": 0, "c": [0, 4, 6, 10, 25, 28, 29, 48, 168, 169, 173], "3": [0, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 26, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 55, 56, 57, 58, 61, 62, 63, 65, 66, 69, 71, 72, 75, 76, 77, 80, 82, 83, 84, 87, 88, 98, 114, 123, 166, 167, 168, 169, 173, 174], "non": [0, 2, 3, 4, 6, 10, 11, 12, 15, 16, 17, 24, 25, 32, 33, 34, 45, 46, 47, 61, 62, 63, 69, 71, 72, 77, 84, 88, 140, 173], "profit": 0, "chariti": 0, "unit": [0, 3, 111], "state": [0, 6, 30, 31], "ar": [0, 1, 2, 3, 4, 6, 7, 9, 10, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 54, 55, 56, 58, 59, 60, 61, 62, 63, 65, 66, 67, 69, 70, 73, 75, 76, 80, 81, 82, 107, 108, 110, 120, 133, 146, 156, 163, 165, 166, 167, 168, 169, 173, 174], "tax": 0, "deduct": 0, "allow": [0, 2, 6, 36, 38, 60, 65, 170, 173, 174], "law": 0, "As": [0, 3, 4, 173, 174], "ani": [0, 3, 4, 6, 14, 20, 25, 36, 37, 38, 39, 41, 43, 44, 45, 46, 47, 48, 49, 53, 57, 59, 61, 62, 63, 64, 65, 67, 68, 74, 101, 139, 163, 168, 173, 174], "should": [0, 2, 3, 4, 6, 25, 27, 36, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 70, 120, 168], "consult": 0, "your": [0, 3, 168, 169, 172, 173], "person": [0, 26], "advis": 0, "ir": 0, "particular": [0, 3, 174], "situat": 0, "thi": [1, 2, 3, 4, 6, 7, 8, 9, 13, 14, 17, 18, 19, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 79, 98, 112, 119, 120, 130, 133, 145, 163, 168, 169, 170, 171, 172, 173, 174], "page": [1, 3, 169, 170, 172], "provid": [1, 2, 3, 6, 27, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 51, 52, 59, 65, 66, 70, 98, 168, 170, 172, 173, 174], "an": [1, 2, 3, 4, 6, 13, 25, 26, 28, 29, 31, 35, 37, 39, 40, 45, 46, 47, 48, 54, 56, 59, 60, 61, 62, 63, 69, 119, 133, 159, 168, 169, 171, 172, 173, 174], "auto": [1, 3, 37, 39, 40, 45, 46, 47, 49], "gener": [1, 2, 3, 6, 25, 37, 38, 48, 50, 64, 69, 70, 145, 168, 170, 173, 174], "summari": [1, 4, 70, 168, 170], "": [1, 3, 6, 10, 24, 25, 28, 29, 48, 56, 59, 63, 65, 90, 94, 97, 98, 99, 102, 121, 124, 142, 148, 168, 169, 173, 174], "see": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 43, 44, 45, 46, 47, 53, 54, 55, 57, 58, 59, 65, 66, 67, 68, 69, 119, 120, 163, 164, 165, 166, 167, 168, 170, 173, 174], "data": [1, 2, 3, 10, 25, 26, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 65, 66, 69, 70, 94, 98, 119, 120, 145, 164, 166, 167, 169, 170, 171, 172], "deprec": [1, 3, 43, 44, 45, 46, 47, 49, 63, 65, 174], "sinc": [1, 2, 4, 43, 44, 45, 46, 47, 49, 56, 63, 65, 168, 173, 174], "version": [1, 3, 4, 6, 43, 44, 45, 46, 47, 49, 59, 63, 65, 168, 174], "0": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 43, 44, 45, 46, 47, 49, 51, 52, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 84, 147, 150, 163, 164, 166, 167, 168, 169, 170, 171, 172, 173, 174], "9": [1, 4, 6, 10, 13, 14, 28, 29, 40, 43, 44, 45, 46, 47, 49, 56, 65, 166, 167, 168, 169, 170, 173, 174], "function": [1, 2, 3, 6, 7, 8, 9, 21, 22, 23, 24, 25, 27, 36, 37, 38, 41, 43, 44, 45, 46, 47, 49, 53, 55, 56, 58, 59, 65, 68, 70, 164, 165, 166, 167, 168, 170, 173, 174], "us": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 16, 17, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 119, 145, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 174], "bio2zarr": [1, 2, 4, 43, 44, 45, 46, 47, 49, 65, 174], "packag": [1, 25, 43, 44, 45, 46, 47, 49, 59, 65, 170, 174], "For": [1, 2, 3, 4, 6, 19, 45, 46, 47, 49, 54, 65, 66, 79, 146, 166, 168, 173, 174], "more": [1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 44, 45, 46, 47, 52, 55, 57, 58, 59, 61, 62, 63, 66, 67, 69, 70, 120, 163, 164, 165, 166, 167, 168, 170, 173, 174], "low": [1, 25, 170], "level": [1, 3, 25, 36, 45, 46, 47, 67, 163, 168, 170], "control": [1, 3, 40, 41, 46, 67, 70, 163, 168, 172, 173, 174], "convert": [1, 2, 4, 6, 13, 14, 36, 37, 39, 41, 42, 46, 47, 48, 50, 170], "from": [1, 2, 3, 6, 10, 11, 14, 15, 16, 17, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 40, 41, 46, 47, 48, 50, 53, 54, 56, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 74, 97, 98, 99, 110, 113, 119, 133, 135, 136, 138, 147, 157, 163, 168, 170, 172, 173, 174], "scikit": [1, 7, 24, 65, 170, 172, 173, 174], "allel": [1, 2, 4, 7, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 21, 22, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 45, 46, 47, 51, 52, 59, 65, 67, 69, 70, 71, 72, 74, 77, 78, 79, 84, 87, 88, 140, 141, 142, 143, 163, 168, 169, 170, 172, 173, 174], "zarr": [1, 2, 4, 36, 38, 39, 42, 43, 45, 46, 47, 48, 49, 50, 53, 65, 68, 168, 170, 171, 172], "represent": [1, 3, 6, 20, 36, 38, 45, 46, 47, 65, 168, 173, 174], "By": [1, 3, 6, 7, 9, 21, 22, 25, 46, 49, 55, 58, 168, 173, 174], "convent": [1, 3, 4, 168, 170], "name": [1, 2, 3, 4, 6, 8, 10, 11, 12, 13, 15, 16, 17, 18, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46, 47, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 89, 90, 139, 145, 163, 165, 166, 167, 168, 169, 174], "singular": [1, 62, 108], "exampl": [1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 21, 22, 23, 25, 28, 29, 30, 31, 35, 45, 46, 47, 48, 52, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66, 69, 139, 164, 166, 167, 168, 170, 173], "genotype_count": [1, 2, 27], "add": [2, 3, 4, 26, 63, 66, 70, 164, 165, 166, 167, 169, 171, 172], "match": [2, 4, 6, 25, 30, 36, 69, 90, 94, 119, 120], "method": [2, 6, 7, 8, 9, 13, 17, 18, 21, 22, 25, 26, 28, 29, 30, 51, 52, 54, 58, 59, 60, 61, 62, 63, 67, 69, 70, 163, 170, 172, 174], "identity_by_st": [2, 10], "timothymillar": 2, "pr": 2, "1229": 2, "gh": [2, 8], "1227": 2, "updat": [2, 3, 4, 6, 172, 173], "gwa": 2, "tutori": [2, 168], "vcf2zarr": [2, 4], "tomwhit": 2, "1258": 2, "1257": 2, "read": [2, 3, 4, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 49, 65, 69, 168, 170, 172], "vcf": [2, 6, 19, 65, 79, 146, 168, 170, 171, 172], "favour": 2, "1233": 2, "1232": 2, "pin": [2, 3], "1230": 2, "numpi": [2, 3, 4, 6, 7, 8, 9, 12, 16, 21, 22, 28, 29, 52, 55, 56, 58, 63, 66, 69, 168, 173], "cbgen": [2, 172], "1228": 2, "1225": 2, "pedigree_contribut": 2, "1093": 2, "963": 2, "pedigree_sel": 2, "1087": 2, "1033": 2, "endelman": [2, 25], "jannink": [2, 25], "estim": [2, 7, 10, 24, 25, 28, 29, 30, 59, 60, 61, 62, 63, 66, 99, 137], "genomic_relationship": [2, 6, 28, 29], "1100": 2, "1062": 2, "display_pedigre": 2, "1104": 2, "1097": 2, "option": [2, 3, 4, 7, 8, 19, 20, 25, 27, 28, 29, 35, 36, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 58, 60, 62, 63, 64, 65, 66, 68, 69, 70, 166, 167, 168, 173, 174], "count": [2, 4, 9, 15, 16, 17, 18, 21, 22, 25, 27, 40, 67, 71, 74, 79, 87, 140, 146, 163, 168, 173], "variant": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 30, 31, 33, 34, 36, 37, 38, 39, 40, 43, 45, 46, 47, 48, 49, 51, 52, 54, 55, 58, 59, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 93, 98, 100, 103, 104, 105, 106, 107, 108, 111, 113, 114, 121, 123, 124, 131, 132, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 161, 162, 163, 165, 166, 167, 168, 170, 172, 173, 174], "directli": [2, 3, 4, 17, 30, 36, 44, 56, 61, 168, 173], "call": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 40, 45, 46, 47, 55, 56, 58, 59, 67, 69, 70, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 84, 85, 86, 100, 103, 104, 105, 106, 107, 113, 144, 152, 153, 154, 155, 156, 157, 163, 164, 165, 166, 167, 168, 169, 173, 174], "genotyp": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 45, 46, 47, 51, 52, 55, 58, 59, 65, 66, 67, 69, 70, 76, 77, 78, 79, 82, 83, 84, 85, 86, 100, 103, 113, 144, 146, 152, 157, 163, 164, 165, 166, 167, 168, 170, 173, 174], "count_variant_allel": [2, 9, 163, 168, 173], "1119": 2, "1116": 2, "simulate_genedrop": 2, "1139": 2, "1107": 2, "perform": [2, 3, 37, 38, 39, 40, 168, 173, 174], "variant_stat": [2, 4, 168, 169, 173], "sample_stat": [2, 4, 169], "error": [2, 6, 35, 45, 46, 66, 168, 169, 173, 174], "miss": [2, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 23, 25, 30, 40, 41, 45, 46, 47, 56, 57, 59, 64, 67, 70, 71, 72, 73, 74, 75, 76, 78, 79, 80, 82, 84, 88, 140, 163, 170, 173], "handl": [2, 3, 168, 174], "valu": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 43, 44, 45, 46, 47, 48, 49, 51, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 69, 70, 71, 72, 73, 74, 75, 77, 79, 80, 82, 84, 88, 95, 101, 110, 111, 120, 125, 130, 133, 137, 140, 147, 149, 150, 161, 162, 164, 165, 166, 167, 168, 170, 173, 174], "most": [2, 3, 6, 51, 52, 59, 168, 173], "field": [2, 24, 38, 39, 40, 41, 45, 46, 47, 48, 51, 65, 70, 174], "were": [2, 3, 4, 6, 119, 145, 170], "mark": 2, "correspond": [2, 3, 4, 6, 11, 12, 15, 16, 17, 25, 27, 28, 29, 39, 40, 45, 46, 47, 48, 59, 64, 65, 71, 72, 78, 79, 88, 89, 139, 140, 145, 168, 169], "fill": [2, 4, 32, 33, 34, 45, 46, 47, 77], "string": [2, 4, 6, 36, 38, 39, 40, 44, 45, 46, 47, 49, 174], "store": [2, 4, 6, 36, 38, 39, 42, 43, 45, 46, 47, 50, 53, 68, 172, 173, 174], "empti": 2, "rather": [2, 3, 4, 6, 24, 28, 29, 173, 174], "than": [2, 3, 4, 6, 14, 19, 24, 28, 29, 32, 36, 37, 44, 45, 46, 47, 48, 59, 61, 62, 63, 65, 69, 173, 174], "similarli": [2, 173], "integ": [2, 4, 6, 13, 36, 37, 39, 40, 44, 45, 46, 47, 57, 63, 64, 65, 69, 79, 145, 168, 169, 173, 174], "int": [2, 8, 19, 25, 27, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 49, 56, 58, 64, 66, 70, 166, 167, 174], "jeromekelleh": 2, "1190": 2, "1192": 2, "max_str_len": 2, "util": [2, 4, 28, 29, 168, 170, 173], "return": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "python": [2, 4, 6, 48, 165, 168, 174], "arrai": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 37, 39, 40, 45, 46, 47, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66, 69, 79, 89, 112, 139, 166, 167, 169, 170, 173, 174], "scalar": [2, 168], "1086": 2, "1085": 2, "turn": 2, "off": [2, 168, 174], "numba": [2, 48], "cach": 2, "default": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 173, 174], "1191": 2, "1156": 2, "xarrai": [2, 3, 4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 28, 29, 35, 45, 46, 47, 53, 55, 58, 66, 68, 70, 164, 166, 167, 168, 169, 170, 172, 173, 174], "repr": [2, 169], "doctest": [2, 3], "1205": 2, "1204": 2, "avoid": [2, 3, 4, 6, 35, 45, 46, 51, 52, 168, 169, 174], "disabl": [2, 14], "jit": [2, 173], "guvectoris": 2, "1199": 2, "1194": 2, "relationship": [2, 25, 28, 29, 35, 59, 61, 62, 63, 69, 126, 127, 128, 130, 136, 138], "matric": [2, 28, 29], "1072": 2, "956": 2, "pairwise_dist": 2, "doc": [2, 3, 37, 39, 40], "benjefferi": 2, "1145": 2, "1142": 2, "format": [2, 3, 4, 6, 19, 40, 45, 46, 47, 65, 168, 171, 172, 173, 174], "matrix": [2, 6, 10, 25, 28, 29, 30, 35, 51, 52, 54, 56, 59, 61, 62, 63, 69, 96, 108, 110, 125, 126, 127, 128, 130, 133, 135, 136, 138, 159], "pairwis": [2, 6, 10, 25, 28, 29, 30, 56, 59, 63, 122, 129, 137], "1148": 2, "1147": 2, "io": [2, 3, 6, 14, 65, 66, 170, 173, 174], "plink": [2, 6, 54, 168, 172], "write_plink": [2, 42, 173], "1003": 2, "926": [2, 168], "phase": [2, 19, 36, 65, 70, 81], "simulate_genotype_call_dataset": [2, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 52, 55, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 173], "1022": 2, "973": 2, "plink_to_zarr": 2, "zarr_to_plink": [2, 173], "conveni": [2, 4, 26, 36, 39, 42, 45, 50, 70, 168, 173], "1047": 2, "1004": 2, "convert_call_to_index": [2, 173], "1050": 2, "1048": 2, "read_chunk_length": [2, 46, 47], "vcf_to_zarr": [2, 43, 45, 48, 65, 173, 174], "These": [2, 3, 6, 25, 27, 66, 110, 111, 168, 173], "reduc": [2, 46, 47, 56, 168], "memori": [2, 4, 36, 37, 38, 39, 40, 45, 46, 47, 48, 54, 61, 168, 169, 173, 174], "usag": [2, 4, 46, 47, 61, 168, 170], "larg": [2, 3, 26, 30, 45, 46, 47, 51, 52, 168, 170, 173, 174], "sampl": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 45, 46, 47, 48, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 89, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 112, 113, 119, 120, 122, 129, 133, 134, 137, 139, 144, 152, 153, 154, 155, 156, 157, 163, 168, 170, 172, 173, 174], "chunk_length": [2, 36, 38, 43, 45, 46, 47, 174], "1044": 2, "1042": 2, "retain_temp_fil": [2, 46], "1046": 2, "1036": 2, "read_vcf": 2, "1052": 2, "hybrid_relationship": [2, 6, 28], "hybrid_inverse_relationship": [2, 29], "invert_relationship_matrix": [2, 6, 28, 29], "1053": 2, "993": [2, 6], "zarr_array_s": 2, "determin": [2, 3, 7, 37, 49, 56, 168], "size": [2, 4, 6, 7, 8, 9, 12, 16, 18, 21, 22, 24, 25, 26, 35, 37, 39, 40, 44, 45, 46, 47, 48, 49, 52, 55, 56, 58, 63, 66, 79, 164, 166, 167, 168, 169, 170, 173], "storag": [2, 4, 6, 39, 43, 44, 45, 46, 47, 49, 53, 68, 168, 170, 173], "1073": 2, "734": 2, "skipna": [2, 25, 30], "1078": 2, "1076": 2, "additional_variant_field": [2, 70], "1056": 2, "header": [2, 45, 46, 47, 48, 50, 65], "when": [2, 3, 6, 17, 26, 28, 29, 30, 36, 37, 38, 39, 40, 45, 46, 47, 55, 63, 67, 69, 70, 120, 159, 163, 168, 173, 174], "write": [2, 3, 4, 6, 46, 48, 170, 172, 174], "write_vcf": [2, 50, 173], "zarr_to_vcf": [2, 48, 173], "previous": [2, 3], "dataset": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 84, 89, 120, 139, 163, 164, 165, 166, 167, 168, 170], "had": [2, 6], "contain": [2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 39, 40, 41, 47, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 98, 130, 139, 163, 164, 165, 166, 167, 168, 173], "vcf_header": [2, 48, 50], "attribut": [2, 4, 6, 20, 48, 50, 90, 168, 169, 173, 174], "1021": 2, "1020": 2, "contig": [2, 4, 37, 39, 40, 66, 70, 90, 98, 145, 160, 165, 166, 167, 168, 169, 173, 174], "contig_id": [2, 4, 168, 169], "filter": [2, 4, 6, 45, 46, 47, 59, 168, 170, 174], "filter_id": [2, 4], "duplic": [2, 3, 69], "inform": [2, 3, 4, 6, 7, 9, 19, 21, 22, 28, 29, 37, 39, 40, 45, 46, 47, 52, 58, 65, 165, 166, 167, 168, 173, 174], "which": [2, 3, 4, 6, 10, 21, 23, 25, 27, 28, 29, 30, 35, 36, 38, 41, 44, 45, 46, 47, 49, 51, 52, 56, 61, 62, 63, 65, 66, 69, 73, 75, 76, 78, 80, 82, 120, 130, 133, 166, 168, 170, 171, 172, 173, 174], "now": [2, 3, 4, 6, 56, 168, 172, 173], "remov": [2, 4, 6, 23, 25, 26, 36, 38, 52, 57, 66, 169], "futur": [2, 3, 6, 172, 173], "releas": [2, 3, 4, 6, 171, 172, 174], "1054": 2, "1035": 2, "paramet": [2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 173, 174], "founder_indic": [2, 63], "pedigree_kinship": [2, 6], "instead": [2, 6, 36, 38, 63], "founder_kinship": [2, 63], "expect": [2, 4, 6, 60, 61, 63, 133, 134, 137, 173, 174], "full": [2, 4, 6, 28, 29, 39, 40, 41, 42, 59, 61, 63, 168, 173, 174], "kinship": [2, 6, 10, 59, 61, 62, 63, 96, 125, 135, 137, 172], "founder": [2, 6, 61, 62, 63, 69], "ignor": [2, 4, 6, 29, 45, 46, 48, 49, 55, 56, 63, 66, 67, 98, 163, 168], "1075": 2, "1061": 2, "scale": [2, 4, 6, 10, 28, 29, 111, 168, 170, 173, 174], "number": [2, 3, 4, 6, 15, 16, 17, 18, 19, 25, 27, 32, 33, 34, 36, 38, 41, 44, 45, 46, 47, 59, 63, 65, 66, 67, 69, 70, 71, 103, 104, 105, 106, 107, 120, 140, 143, 146, 152, 153, 154, 155, 156, 163, 166, 167, 168, 173, 174], "1028": 2, "1026": 2, "1027": 2, "import": [2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 28, 29, 30, 31, 35, 37, 39, 40, 48, 52, 55, 56, 57, 58, 61, 62, 63, 66, 69, 164, 166, 167, 168, 169, 170, 173, 174], "much": [2, 4, 6, 36, 37, 38, 174], "faster": [2, 4, 63, 173, 174], "due": [2, 3, 6, 60, 168, 174], "defer": 2, "compil": [2, 168, 173], "1039": [2, 3], "939": 2, "wa": [2, 3, 4, 25, 35, 38, 172], "output": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 43, 45, 46, 47, 48, 50, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 173, 174], "file": [2, 3, 4, 6, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 65, 68, 170, 172, 173], "temp_chunk_length": [2, 36, 45, 46, 174], "chunk": [2, 4, 6, 7, 9, 21, 22, 35, 36, 37, 38, 39, 40, 43, 45, 46, 47, 48, 58, 60, 68, 169, 170, 171, 172, 173], "ha": [2, 3, 4, 6, 14, 17, 36, 44, 61, 62, 63, 69, 70, 168, 173, 174], "been": [2, 3, 4, 6, 17, 44, 48, 52, 61, 166, 173], "so": [2, 3, 4, 6, 25, 36, 38, 44, 45, 46, 47, 48, 61, 62, 63, 66, 70, 165, 168, 169, 173, 174], "fail": [2, 37], "zerodivisionerror": 2, "1069": 2, "1068": 2, "correct": [2, 3, 6, 10, 168], "mix": [2, 13, 18, 26, 32, 61, 62, 63, 67, 69, 77, 84, 163, 170], "ploidi": [2, 4, 6, 13, 14, 18, 25, 27, 31, 32, 33, 34, 40, 41, 45, 46, 47, 52, 59, 60, 61, 62, 63, 65, 67, 69, 70, 75, 76, 77, 80, 84, 86, 113, 120, 157, 163, 168, 169, 170, 173], "display_genotyp": [2, 4, 10, 11, 12, 13, 15, 16, 17, 18, 23, 30, 31, 69, 168, 169, 173], "1030": 2, "571": 2, "813": 2, "801": 2, "pedigre": [2, 10, 20, 28, 29, 40, 41, 57, 60, 61, 62, 63, 64, 69, 133, 134, 135, 136, 137, 138], "parent": [2, 6, 20, 57, 60, 61, 62, 63, 64, 69, 94, 95, 119, 120], "child": 2, "pedigree_inbreed": 2, "pedigree_inverse_kinship": 2, "786": 2, "implement": [2, 4, 6, 8, 24, 26, 59, 61, 168, 172], "calcul": [2, 4, 6, 7, 9, 17, 21, 22, 27, 28, 29, 30, 35, 44, 52, 55, 56, 57, 58, 60, 61, 62, 113, 135, 136, 157, 163, 164, 165, 166, 167], "vanraden": [2, 25], "genom": [2, 25, 28, 29, 40, 44, 45, 46, 47, 49, 60, 61, 63, 66, 120, 125, 126, 133, 164, 166, 168, 170, 172], "903": 2, "874": 2, "cohort": [2, 7, 8, 9, 12, 16, 21, 22, 26, 55, 58, 87, 88, 101, 114, 115, 116, 117, 118, 121, 123, 124, 131, 132, 170], "sum": [2, 4, 6, 10, 52, 69, 120, 168, 173], "mean": [2, 3, 4, 6, 8, 25, 36, 38, 45, 46, 47, 49, 55, 58, 66, 166, 168, 174], "867": 2, "730": 2, "toggl": 2, "environ": [2, 170, 173, 174], "variabl": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 45, 46, 47, 48, 51, 52, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 163, 164, 165, 166, 167, 168, 170, 174], "sgkit_disable_numba_cach": [2, 173], "870": 2, "869": 2, "window_by_genom": [2, 168], "whole": [2, 6, 54, 66, 164, 168, 174], "statist": [2, 3, 4, 7, 8, 9, 21, 22, 24, 25, 26, 55, 58, 66, 67, 70, 115, 116, 117, 118, 122, 132, 151, 163, 164, 165, 166, 167, 168, 172, 173, 174], "945": 2, "893": 2, "window_by_interv": 2, "creat": [2, 3, 4, 6, 37, 48, 64, 65, 168, 170, 173, 174], "window": [2, 7, 8, 9, 21, 22, 51, 52, 55, 58, 114, 115, 116, 117, 118, 121, 123, 124, 131, 132, 160, 161, 162, 164, 165, 166, 167, 170, 173, 174], "arbitrari": [2, 4, 165], "interv": [2, 31, 90, 91, 92, 165, 168, 173], "974": 2, "contig_length": [2, 4], "found": [2, 3, 6, 25], "946": 2, "464": 2, "export": [2, 170, 173], "953": 2, "924": 2, "auto_rechunk": [2, 68], "save_dataset": [2, 39, 169, 173], "automat": [2, 3, 6, 18, 27, 29, 66, 68, 173], "rechunk": [2, 26, 36, 38, 43, 46, 56, 68, 169, 173, 174], "befor": [2, 3, 4, 7, 8, 9, 21, 22, 55, 58, 63, 68, 168, 173], "save": [2, 68, 170, 173], "disk": [2, 36, 38, 39, 42, 46, 47, 168, 174], "necessari": [2, 3, 4, 23, 26, 37, 68, 173, 174], "requir": [2, 3, 6, 8, 25, 28, 30, 38, 59, 60, 61, 62, 63, 68, 69, 168, 169, 173, 174], "equal": [2, 6, 14, 27, 36, 40, 41, 44, 46, 47, 61, 62, 63, 64, 166, 169, 174], "988": 2, "981": 2, "gene": [2, 69], "\u03b5": [2, 24], "set": [2, 4, 6, 14, 25, 26, 27, 36, 38, 39, 40, 41, 42, 45, 46, 47, 49, 52, 54, 56, 66, 112, 166, 168, 169, 170, 173, 174], "associ": [2, 4, 26, 66, 149, 168, 172], "analysi": [2, 4, 6, 23, 25, 26, 46, 47, 59, 69, 168, 172, 174], "975": 2, "692": 2, "count_variant_genotyp": [2, 27, 163], "occurr": [2, 4, 11, 12, 15, 16, 17, 71, 72, 88, 140, 141, 143, 163], "each": [2, 3, 4, 6, 11, 12, 13, 15, 16, 17, 18, 20, 25, 26, 27, 32, 33, 34, 44, 45, 46, 49, 51, 56, 57, 60, 61, 62, 63, 64, 66, 69, 70, 71, 72, 73, 75, 77, 78, 79, 80, 81, 82, 85, 88, 101, 109, 110, 113, 120, 133, 140, 141, 145, 146, 147, 149, 151, 157, 160, 163, 165, 166, 167, 168, 169, 173, 174], "possibl": [2, 3, 4, 6, 18, 66, 74, 142, 146, 168, 170, 173, 174], "911": 2, "1002": 2, "927": 2, "802": 2, "The": [2, 3, 4, 8, 10, 18, 19, 21, 23, 25, 26, 27, 28, 29, 30, 35, 36, 38, 40, 43, 44, 45, 46, 47, 48, 49, 50, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 65, 67, 69, 70, 100, 101, 102, 103, 104, 105, 106, 107, 119, 120, 128, 130, 141, 142, 143, 144, 146, 148, 152, 153, 154, 155, 156, 158, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174], "count_a1": [2, 40], "read_plink": [2, 39, 173], "true": [2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 74, 163, 164, 165, 166, 167, 168, 173], "fals": [2, 4, 6, 25, 28, 29, 35, 37, 39, 40, 45, 46, 47, 61, 62, 63, 64, 66, 68, 69, 164, 166, 167, 168, 169, 173], "furthermor": [2, 174], "longer": 2, "clear": [2, 3], "how": [2, 3, 4, 5, 6, 48, 63, 168, 170, 173, 174], "behav": [2, 168], "952": 2, "947": 2, "dosag": [2, 4, 6, 25, 26, 36, 38, 51, 52, 66, 74, 174], "specif": [2, 3, 4, 40, 41, 45, 46, 47, 59, 70, 79, 146, 168, 170, 171, 172, 174], "all": [2, 3, 4, 6, 8, 10, 14, 18, 25, 28, 29, 30, 33, 34, 36, 38, 39, 40, 41, 42, 48, 52, 55, 56, 58, 60, 61, 62, 63, 64, 66, 69, 70, 81, 89, 113, 120, 122, 129, 139, 143, 157, 163, 168, 169, 173, 174], "refer": [2, 3, 4, 10, 18, 19, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 45, 50, 59, 61, 62, 63, 66, 67, 69, 84, 106, 107, 112, 146, 155, 156, 158, 163, 168, 170, 173, 174], "have": [2, 3, 4, 6, 20, 25, 26, 27, 28, 29, 44, 45, 46, 47, 48, 49, 52, 60, 61, 62, 63, 65, 66, 69, 166, 168, 169, 172, 173, 174], "replac": [2, 6, 23, 25, 31, 64, 76, 119, 168, 173], "call_dosage_spec": [2, 25, 26, 37, 51, 52, 66], "includ": [2, 3, 4, 6, 7, 18, 28, 29, 35, 36, 38, 39, 40, 41, 42, 48, 50, 51, 57, 64, 69, 120, 168, 172, 173, 174], "encod": [2, 4, 6, 36, 38, 45, 46, 47, 61, 63, 74, 79, 84, 119, 168, 171, 172, 174], "addition": [2, 26], "ld_matrix": [2, 52, 54], "ld_prune": 2, "call_dosag": [2, 4, 6, 25, 51, 52, 66, 74], "995": [2, 6, 168], "875": 2, "variant_genotype_count_spec": [2, 18, 27], "follow": [2, 3, 4, 6, 8, 14, 24, 25, 28, 29, 36, 37, 39, 40, 41, 42, 45, 46, 47, 50, 56, 61, 62, 63, 65, 66, 67, 69, 70, 79, 146, 163, 164, 165, 166, 167, 168, 173, 174], "order": [2, 3, 4, 6, 14, 18, 23, 25, 28, 54, 57, 63, 146, 173], "e": [2, 6, 18, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 51, 52, 56, 60, 61, 63, 67, 69, 74, 108, 109, 110, 163, 168, 173, 174], "homozyg": [2, 4, 6, 27, 67, 105, 106, 107, 146, 154, 155, 156, 163], "heterozyg": [2, 4, 6, 27, 67, 104, 146, 153, 163, 168], "altern": [2, 4, 6, 19, 25, 27, 45, 46, 47, 65, 67, 74, 79, 105, 146, 154, 163, 168, 169, 173], "biallel": [2, 4, 6, 25, 27, 41, 59, 79, 146, 173], "diploid": [2, 4, 6, 8, 19, 25, 27, 31, 36, 37, 38, 41, 59, 60, 61, 62, 63, 69, 146, 174], "hardy_weinberg_test": [2, 4, 169], "pars": [2, 174], "933": 2, "compress": [2, 36, 38, 44, 45, 46, 47, 48, 49, 168, 170], "937": 2, "925": 2, "ensur": [2, 3, 6], "excess": [2, 54], "dimens": [2, 4, 6, 7, 9, 10, 18, 21, 22, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 43, 45, 46, 47, 48, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 69, 119, 120, 161, 162, 164, 165, 166, 167, 168, 169, 173, 174], "943": 2, "asv": [2, 3], "benchmark": [2, 170, 174], "976": 2, "978": 2, "837": 2, "836": 2, "vlenutf8": 2, "doubl": [2, 3, 61, 63], "852": [2, 4], "785": 2, "input": [2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 45, 46, 47, 48, 49, 50, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 69, 163, 164, 165, 166, 167, 173, 174], "weir_goudet_beta": [2, 6], "865": 2, "861": 2, "get_region_start": 2, "work": [2, 3, 4, 168, 170, 172, 174], "colon": 2, "dash": 2, "d": [2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 41, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 121, 163, 164, 165, 166, 167, 168, 169, 173, 174], "laub": 2, "883": 2, "882": 2, "hypothesi": 2, "test": [2, 4, 6, 23, 24, 27, 66, 147, 170, 173], "972": 2, "bug": 3, "report": [3, 4, 26], "fix": [3, 25, 32, 45, 46, 47, 65, 168, 173, 174], "improv": [3, 6, 25, 168, 174], "enhanc": 3, "idea": [3, 174], "welcom": 3, "resourc": [3, 168, 173], "best": [3, 6, 66, 99], "part": [3, 44, 45, 46, 49, 174], "came": 3, "dask": [3, 4, 6, 37, 39, 40, 46, 47, 48, 56, 65, 168, 169, 170, 173, 174], "guidelin": [3, 168], "convers": [3, 46, 47, 65, 173], "about": [3, 4, 6, 52, 168, 170, 174], "happen": 3, "place": [3, 48, 168, 174], "github": [3, 4, 45, 46, 47, 65], "tracker": 3, "around": [3, 6, 53, 68, 166, 174], "new": [3, 4, 6, 23, 48, 64, 168, 170, 172, 173], "featur": [3, 168, 173, 174], "question": [3, 6, 172], "do": [3, 6, 28, 29, 66, 168, 170, 174], "x": [3, 4, 6, 56, 133, 168, 169, 173], "what": 3, "wai": [3, 168, 173, 174], "y": [3, 4, 133], "genet": [3, 4, 6, 10, 24, 25, 26, 27, 28, 29, 51, 52, 59, 61, 62, 63, 66, 69, 123, 124, 172, 174], "tend": 3, "higher": [3, 46, 47, 168, 173, 174], "theme": 3, "detail": [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 45, 50, 55, 57, 58, 59, 66, 67, 69, 163, 164, 165, 166, 167, 168, 170, 173], "pull": 3, "request": [3, 4, 6, 173, 174], "maintain": 3, "few": [3, 4, 6, 168, 170, 173, 174], "host": [3, 173], "dev": [3, 4, 169, 173], "organ": 3, "primari": [3, 6, 168], "sever": [3, 6, 59, 74, 168, 173], "other": [3, 6, 7, 25, 48, 56, 60, 61, 62, 63, 70, 74, 168, 170, 172, 174], "differ": [3, 4, 6, 168, 173, 174], "compon": [3, 4, 24, 59, 108, 109, 110, 111, 112], "A": [3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 73, 75, 77, 78, 80, 81, 82, 101, 163, 164, 165, 166, 167, 168, 169, 173, 174], "exhaust": 3, "list": [3, 4, 43, 45, 46, 47, 66, 168, 170, 173, 174], "main": [3, 168, 174], "algorithm": [3, 38, 54, 56, 168, 172, 174], "can": [3, 4, 6, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 56, 61, 62, 63, 68, 74, 111, 120, 164, 168, 169, 173, 174], "challeng": 3, "first": [3, 4, 6, 19, 24, 25, 28, 29, 30, 37, 39, 40, 43, 45, 46, 47, 59, 64, 65, 84, 168, 169, 173, 174], "fortun": [3, 6], "good": [3, 45, 46, 49, 56, 170, 174], "materi": [3, 54, 169], "exist": [3, 4, 6, 37, 173], "internet": 3, "repeat": [3, 7, 8, 9, 12, 16, 21, 22, 55, 58, 168], "here": [3, 4, 6, 168, 173, 174], "we": [3, 4, 6, 168, 172, 173, 174], "panda": [3, 4, 6, 168, 169, 170, 173], "link": 3, "subject": [3, 4, 6], "http": [3, 4, 6, 37, 38, 39, 40, 45, 46, 47, 65, 66, 173], "pydata": [3, 168], "org": [3, 6, 37, 39, 40, 66], "stabl": 3, "html": [3, 37, 39, 40, 66], "track": [3, 173, 174], "known": [3, 6, 10, 57, 63, 124, 166], "potenti": [3, 6, 168], "identifi": [3, 4, 6, 26, 37, 40, 41, 57, 69, 94, 102, 148], "rais": [3, 6, 8, 13, 18, 20, 25, 27, 28, 29, 40, 41, 44, 45, 46, 47, 51, 52, 54, 57, 59, 60, 61, 62, 63, 66, 67, 69, 163, 166, 173, 174], "start": [3, 4, 6, 48, 50, 91, 161, 164, 165, 166, 167, 170, 172, 174], "public": 3, "look": [3, 4, 6, 170, 174], "introductori": 3, "get": [3, 6, 52, 170], "out": [3, 4, 46, 48, 49, 66, 98, 99, 168, 169, 173], "label": [3, 56, 168], "familiar": 3, "some": [3, 4, 6, 145, 164, 165, 166, 167, 168, 169, 173, 174], "parallel": [3, 45, 46, 49, 168, 173, 174], "assum": [3, 10, 19, 28, 29, 32, 60, 61, 62, 63, 139, 174], "sure": 3, "cover": [3, 6, 174], "plan": 3, "produc": [3, 6, 43, 66, 70, 168, 174], "assign": [3, 18, 27, 168, 169], "yourself": 3, "indic": [3, 6, 28, 29, 35, 51, 57, 61, 62, 63, 73, 74, 75, 77, 78, 79, 80, 81, 82, 84, 95, 101, 113, 130, 157, 168, 173, 174], "In": [3, 6, 48, 108, 145, 168, 169, 173, 174], "mention": 3, "relat": [3, 6, 10, 59, 63, 96, 168, 172], "fork": 3, "clone": [3, 61, 62, 63], "com": [3, 4, 6], "usernam": 3, "made": [3, 14], "submit": [3, 173], "pip": [3, 168, 173, 174], "cd": 3, "r": [3, 4, 6, 25, 27, 28, 29, 59, 66], "txt": [3, 4, 6], "nvidia": 3, "gpu": [3, 56, 168], "need": [3, 4, 6, 25, 37, 38, 40, 45, 46, 47, 65, 168, 169, 173, 174], "configur": [3, 174], "properli": 3, "cudatoolkit": 3, "instruct": [3, 173, 174], "same": [3, 4, 6, 7, 19, 21, 28, 29, 36, 63, 66, 167, 168, 173, 174], "also": [3, 4, 6, 36, 37, 38, 40, 45, 46, 49, 56, 61, 62, 63, 64, 111, 119, 120, 124, 145, 166, 168, 169, 172, 173, 174], "pre": 3, "commit": 3, "enforc": 3, "pytest": 3, "directori": [3, 4, 36, 38, 39, 42, 43, 45, 46, 47, 50, 53, 68], "similar": [3, 4, 173], "languag": 3, "style": [3, 4], "action": 3, "ci": 3, "servic": 3, "everi": [3, 56, 168, 174], "push": 3, "coverag": 3, "build": [3, 168], "emploi": 3, "extens": [3, 4, 39, 40, 41, 42], "both": [3, 6, 25, 26, 44, 45, 46, 49, 60, 61, 63, 166, 168, 170, 173, 174], "todai": 3, "must": [3, 6, 8, 13, 14, 15, 18, 25, 26, 27, 28, 29, 32, 33, 34, 36, 38, 39, 40, 41, 42, 44, 45, 46, 51, 52, 59, 61, 62, 63, 66, 67, 69, 70, 89, 90, 119, 120, 139, 163, 165, 166, 169, 174], "100": [3, 4, 36, 48, 66, 168, 169, 173, 174], "accept": [3, 172, 174], "measur": [3, 166, 167, 168], "local": [3, 4, 6, 36, 173, 174], "machin": [3, 48, 173, 174], "cov": 3, "written": [3, 4, 46, 48, 50], "htmlcov": 3, "show": [3, 4, 5, 6, 38, 48, 168, 173, 174], "line": [3, 48, 50, 173], "suit": 3, "live": 3, "filenam": [3, 173], "test_": 3, "modul": [3, 173], "py": [3, 6, 173], "underscor": 3, "group": [3, 4, 168], "def": [3, 4, 173], "test_foo__accepts_empty_input": 3, "test_foo__accepts_str": 3, "user": [3, 45, 74, 168, 170], "face": 3, "numpydoc": 3, "section": [3, 45, 46, 47, 65, 174], "explanatori": 3, "prose": 3, "ad": [3, 6, 24, 26, 39, 40, 41, 42, 48, 168, 170], "thei": [3, 4, 6, 26, 41, 56, 168, 173, 174], "onli": [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 52, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 168, 169, 173, 174], "hint": [3, 44], "rst": 3, "them": [3, 4, 6, 168, 173, 174], "access": [3, 4, 6, 168, 170, 174], "reproduc": 3, "valuabl": 3, "importantli": [3, 6], "common": [3, 4, 6, 59, 145, 168, 169, 172], "trump": 3, "case": [3, 6, 21, 31, 40, 41, 45, 46, 47, 48, 65, 120, 168, 173, 174], "take": [3, 4, 6, 45, 46, 49, 168, 174], "preced": 3, "over": [3, 37, 45, 46, 49, 165, 166, 167, 168, 170, 174], "space": [3, 38, 166, 168, 174], "To": [3, 4, 6, 7, 8, 9, 21, 22, 55, 56, 58, 168, 173, 174], "skip": [3, 25, 30, 174], "comment": [3, 4, 6, 168, 169, 173], "after": [3, 4, 6, 45, 46, 173], "becaus": [3, 6, 36, 48, 168, 173, 174], "setup": [3, 173], "cfg": 3, "succe": 3, "chang": [3, 4, 6, 45, 46, 47], "pass": [3, 4, 20, 23, 24, 36, 37, 39, 40, 49, 53, 56, 68, 173, 174], "It": [3, 4, 6, 48, 168, 173, 174], "tool": [3, 48, 168, 170, 173], "black": [3, 4], "flake8": 3, "consist": [3, 6, 173, 174], "isort": 3, "mypi": 3, "static": 3, "manual": [3, 6, 45, 173, 174], "adher": 3, "without": [3, 4, 6, 25, 31, 38, 48, 66, 119, 164, 166, 167, 168, 169, 173, 174], "etc": [3, 66, 173], "omit": [3, 36, 38, 48, 56, 81], "current": [3, 7, 8, 9, 21, 22, 26, 27, 28, 29, 37, 40, 45, 46, 49, 58, 60, 174], "rebas": 3, "squash": 3, "merg": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167, 168], "strategi": 3, "certain": [3, 38], "practic": [3, 6, 168], "life": 3, "easier": [3, 4, 53, 68, 168, 169, 173], "try": [3, 173], "isol": [3, 168], "singl": [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 40, 43, 44, 46, 49, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 79, 119, 163, 164, 165, 166, 167, 168, 173, 174], "guarante": [3, 174], "speedi": 3, "meaning": 3, "small": [3, 4, 30, 46, 47, 169, 173, 174], "again": [3, 4, 173], "buggi": 3, "veri": [3, 4, 45, 46, 47, 51, 52, 173, 174], "handi": [3, 173], "interact": [3, 168], "runtim": [3, 46, 47], "one": [3, 4, 6, 14, 25, 26, 29, 40, 41, 44, 47, 48, 61, 62, 63, 74, 168, 173, 174], "don": [3, 6, 172, 174], "t": [3, 4, 6, 25, 26, 28, 29, 39, 40, 151, 168, 169, 172, 173, 174], "forget": 3, "keep": 3, "exclud": [3, 59], "minimum": [3, 173], "sometim": [3, 6, 168, 174], "unavoid": 3, "conflict": 3, "manag": [3, 168, 173], "conda": [3, 168, 173, 174], "forg": [3, 168], "feedstock": 3, "There": [3, 4, 168, 173, 174], "night": 3, "against": [3, 4, 66], "branch": [3, 58, 132], "kei": [3, 20, 36, 45, 46, 47, 56, 65, 174], "upstream": [3, 173], "find": [3, 44, 52, 170, 174], "break": [3, 174], "would": [3, 6, 168, 173, 174], "affect": [3, 6], "problem": 3, "librari": [3, 4, 6, 20, 168, 172, 174], "sphinx": 3, "restructuredtext": 3, "markup": 3, "graphviz": [3, 20], "dot": 3, "execut": [3, 168], "result": [3, 4, 6, 13, 17, 25, 35, 36, 38, 39, 40, 52, 56, 57, 61, 62, 63, 65, 66, 69, 70, 98, 110, 119, 168, 170, 173, 174], "end": [3, 6, 168, 174], "up": [3, 48, 64, 173, 174], "_build": 3, "edit": [3, 4, 26], "warn": [3, 4, 173], "clean": 3, "sphinxopt": 3, "w": [3, 4, 24, 28, 29, 69, 173], "go": 3, "n": [3, 4, 6, 25, 26, 27, 28, 29, 56, 71, 72, 74, 76, 77, 78, 79, 81, 84, 85, 88, 89, 93, 94, 95, 97, 98, 99, 108, 110, 119, 120, 125, 126, 129, 130, 131, 133, 137, 139, 140, 145, 146, 159, 168], "airspe": 3, "veloc": 3, "micro": 3, "via": [3, 69, 168, 173], "itself": 3, "recip": 3, "defin": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 45, 46, 47, 51, 52, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 74, 90, 108, 111, 146, 163, 165, 166, 167, 168, 170, 173], "conf": 3, "json": [3, 4], "readthedoc": [3, 38, 66], "en": [3, 37, 38, 39, 40, 66], "writing_benchmark": 3, "upload": 3, "seen": [3, 168], "site": [3, 31], "config": [3, 56, 173], "publish": [3, 6], "v": [3, 4, 6, 28, 29, 59], "browser": 3, "server": 3, "preview": 3, "roughli": [3, 44, 66, 174], "arch": 3, "x86_64": 3, "cpu": [3, 56, 173], "intel": 3, "xeon": 3, "platinum": 3, "8272cl": 3, "2": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 40, 41, 45, 46, 47, 51, 52, 55, 56, 59, 60, 61, 62, 63, 65, 66, 69, 70, 73, 74, 78, 79, 81, 84, 85, 86, 89, 94, 95, 96, 98, 99, 108, 111, 112, 115, 116, 117, 118, 119, 120, 121, 122, 124, 125, 126, 127, 128, 129, 130, 131, 133, 135, 136, 137, 138, 139, 140, 141, 142, 146, 149, 150, 151, 164, 166, 167, 168, 169, 170, 173, 174], "60ghz": 3, "fv": 3, "az183": 3, "669": [3, 4], "num_cpu": 3, "o": [3, 26, 27, 90, 94, 102, 142, 148, 173], "linux": [3, 173], "5": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 16, 21, 22, 25, 27, 28, 29, 30, 35, 52, 55, 56, 58, 59, 60, 62, 63, 66, 69, 166, 167, 168, 169, 171, 172, 173, 174], "4": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 31, 45, 46, 47, 48, 52, 55, 56, 59, 61, 62, 63, 65, 69, 97, 132, 166, 167, 168, 169, 173, 174], "azur": [3, 173], "ram": 3, "7121276": 3, "1": [3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 40, 41, 45, 46, 47, 48, 51, 55, 56, 57, 59, 60, 61, 62, 63, 64, 65, 66, 69, 70, 78, 79, 84, 89, 90, 91, 92, 93, 97, 99, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 113, 133, 134, 139, 143, 144, 145, 147, 148, 150, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 164, 166, 167, 168, 169, 170, 173, 174], "abov": [3, 4, 6, 36, 38, 51, 52, 56, 168, 173], "command": [3, 4, 173], "ye": 3, "doe": [3, 4, 6, 7, 9, 13, 18, 21, 22, 37, 48, 58, 61, 62, 63, 65, 66, 67, 69, 98, 163, 174], "slightli": [3, 4, 6, 51, 52], "could": [3, 6], "sai": 3, "30ghz": 3, "less": [3, 6, 14, 32, 44, 48, 59, 145, 169, 174], "huge": 3, "deviat": 3, "though": [3, 6, 168, 170], "unless": [3, 17], "custom": [3, 74, 168], "henc": [3, 6, 23, 174], "minor": [3, 6, 51, 52, 59], "consum": 3, "pinch": 3, "salt": 3, "approv": 3, "least": [3, 6, 10, 14, 51, 52, 61, 62, 63, 66, 98], "mergifi": 3, "autom": 3, "flow": 3, "committ": 3, "decid": [3, 56], "topic": [3, 6], "mai": [3, 6, 10, 25, 28, 29, 37, 38, 44, 45, 46, 47, 49, 57, 61, 62, 63, 66, 69, 119, 130, 145, 166, 168, 169, 170, 173, 174], "understand": [3, 173, 174], "histori": 3, "behind": [3, 4, 174], "choic": [3, 4], "within": [3, 6, 25, 31, 35, 37, 40, 41, 55, 57, 61, 62, 63, 65, 70, 77, 119, 120, 139, 165, 166, 168, 170, 173, 174], "far": [3, 4], "debat": 3, "whether": [3, 36, 37, 38, 39, 40, 51, 66, 70], "object": [3, 4, 6, 19, 36, 48, 50, 168, 169, 173, 174], "put": 3, "layer": [3, 4, 6], "encapsul": 3, "16": [3, 4, 24, 28, 29, 56, 59, 168, 169, 173, 174], "78": [3, 4], "bring": 3, "stricter": 3, "43": [3, 168, 173], "124": [3, 69], "276": 3, "295": [3, 29], "saniti": 3, "effici": [3, 6, 17, 25, 26, 28, 29, 30, 61, 66, 168, 174], "why": [3, 4], "those": [3, 6, 18, 25, 51, 52, 61, 62, 63, 69, 70, 94, 119, 120, 168, 170, 173], "61": [3, 4, 168], "97": [3, 4, 168], "propos": 3, "243": 3, "learn": [3, 24, 26, 173], "effect": [3, 6, 14, 24, 26, 28, 29, 66, 98, 168], "114": 3, "348": 3, "init": 3, "accommod": 3, "__all__": 3, "declar": [3, 4, 173], "decis": 3, "251": 3, "notebook": [4, 5, 6, 173], "port": 4, "hail": [4, 170], "demonstr": [4, 6, 168, 173], "run": [4, 26, 38, 46, 47, 56, 168, 173], "wide": [4, 6, 172], "snp": [4, 6, 24, 59], "reader": 4, "encourag": 4, "alongsid": 4, "background": 4, "motiv": [4, 6], "step": [4, 6, 8, 28, 29, 46, 56, 166, 167, 168, 173, 174], "note": [4, 6, 23, 27, 38, 40, 45, 46, 47, 52, 65, 70, 168, 173, 174], "exactli": [4, 44, 174], "still": [4, 6, 23, 170, 174], "its": [4, 6, 25, 61, 63, 64, 69, 168, 173, 174], "api": [4, 6, 37, 39, 40, 56, 168, 169, 170], "backward": [4, 6], "compat": [4, 6, 59, 168], "sg": [4, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 28, 29, 30, 31, 35, 52, 55, 57, 58, 61, 62, 63, 69, 164, 166, 167, 168, 169, 173, 174], "standard": [4, 6, 44, 48, 66, 168, 173, 174], "displai": [4, 19, 20, 168, 173], "np": [4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 52, 55, 56, 58, 66, 69, 166, 168, 169, 173, 174], "pd": [4, 6], "xr": [4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 28, 29, 35, 55, 58, 60, 64, 168], "set_opt": 4, "display_expand_attr": 4, "display_expand_data_var": 4, "20mb": [4, 45, 46, 49], "portion": 4, "pathlib": [4, 6], "path": [4, 6, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 65, 68], "1kg": [4, 174], "bgz": [4, 174], "respons": [4, 6], "googleapi": [4, 6], "wb": [4, 6], "f": [4, 6, 28, 29, 58, 61, 72, 74, 83, 85, 88, 96, 97, 98, 99, 100, 108, 109, 110, 111, 112, 114, 115, 116, 117, 118, 119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 141, 144, 147, 150, 159, 169, 173, 174], "content": [4, 6, 40, 66], "tbi": [4, 44, 45, 46, 47, 49, 174], "next": [4, 6], "filesystem": [4, 174], "vcz": 4, "bash": [4, 173], "explod": 4, "forc": [4, 168], "icf": 4, "mkschema": 4, "schema": 4, "hand": 4, "scan": [4, 172], "00": [4, 56, 146, 173], "bcf_hdr_check_san": 4, "pl": 4, "g": [4, 6, 25, 28, 29, 36, 37, 38, 44, 45, 46, 47, 51, 52, 60, 61, 62, 63, 67, 69, 74, 79, 163, 168, 169, 174], "59file": 4, "10": [4, 6, 10, 13, 19, 45, 46, 47, 52, 56, 66, 164, 166, 167, 168, 169, 170, 173, 174], "9k": 4, "var": 4, "66": [4, 168], "654var": 4, "281": [4, 29, 173], "07": 4, "43kvar": 4, "495": 4, "06": [4, 24, 66], "68kvar": 4, "7": [4, 6, 10, 13, 36, 38, 45, 46, 47, 56, 62, 63, 167, 168, 169, 170, 173, 174], "709": 4, "05": [4, 13, 25], "81kvar": 4, "8": [4, 6, 10, 13, 59, 166, 167, 168, 169, 170, 173, 174], "909": 4, "01": [4, 6, 28, 56, 59, 146, 171], "85kvar": 4, "03k": 4, "02": [4, 56, 146], "17": [4, 62, 168, 169, 173], "576var": 4, "11": [4, 6, 25, 56, 146, 168, 169, 173], "25k": 4, "13": [4, 56, 168, 169, 173], "696var": 4, "14": [4, 56, 168, 169, 173], "47k": 4, "810var": 4, "69k": 4, "918var": 4, "84k": 4, "03": [4, 56], "15": [4, 168, 169, 173], "570var": 4, "19": [4, 13, 66, 168, 169, 173], "07k": 4, "650var": 4, "21": [4, 6, 56, 166, 168, 169, 173, 174], "29k": 4, "730var": 4, "23": [4, 56, 168, 169, 173, 174], "49k": 4, "801var": 4, "24": [4, 56, 168, 170, 173], "65k": 4, "04": [4, 56, 173], "578var": 4, "26": [4, 168, 173], "80k": 4, "529var": 4, "28": [4, 168, 173], "02k": 4, "595var": 4, "29": [4, 168, 173], "17k": 4, "514var": 4, "31": [4, 56, 168, 173], "39k": 4, "575var": 4, "33": [4, 56, 168, 173], "61k": 4, "638var": 4, "35": [4, 13, 63, 168, 173], "78k": 4, "680var": 4, "36": [4, 168, 173], "94k": 4, "12": [4, 6, 56, 146, 166, 168, 169, 173, 174], "544var": 4, "38": [4, 168, 173], "603var": 4, "40": [4, 166, 168, 173], "09": 4, "663var": 4, "42": [4, 168, 173], "54k": 4, "08": [4, 171], "535var": 4, "44": [4, 13, 168, 173], "77k": 4, "591var": 4, "46": [4, 168, 173], "99k": 4, "649var": 4, "47": [4, 26, 168, 173], "16k": 4, "546var": 4, "49": [4, 168, 173], "38k": 4, "600var": 4, "51": [4, 168, 173], "53k": 4, "480var": 4, "53": [4, 168], "75k": 4, "530var": 4, "54": [4, 168], "92k": 4, "565var": 4, "56": [4, 168], "6": [4, 6, 10, 13, 24, 25, 52, 56, 58, 62, 63, 166, 167, 168, 169, 170, 173, 174], "506var": 4, "58": [4, 168], "556var": 4, "59": [4, 168], "45k": 4, "592var": 4, "511var": 4, "63": [4, 168], "81k": 4, "65": [4, 63, 168], "606var": 4, "513var": 4, "68": [4, 168], "70": 4, "59k": 4, "612var": 4, "71": [4, 28, 29], "74k": 4, "519var": 4, "73": [4, 28, 29], "560var": 4, "74": 4, "08k": 4, "76": [4, 27], "23k": 4, "477var": 4, "77": 4, "36k": 4, "456var": 4, "79": 4, "507var": 4, "80": 4, "72k": 4, "463var": 4, "82": 4, "95k": 4, "83": 4, "465var": 4, "85": 4, "30k": 4, "516var": 4, "87": 4, "43k": 4, "470var": 4, "89": 4, "63k": 4, "90": [4, 26], "18": [4, 59, 168, 169, 173], "472var": 4, "92": [4, 28, 29], "97k": 4, "523var": 4, "93": [4, 27, 28, 29], "1k": 4, "478var": 4, "95": [4, 168], "3k": 4, "96": [4, 168, 173], "4k": 4, "469var": 4, "5k": 4, "20": [4, 13, 38, 56, 168, 169, 173, 174], "445var": 4, "98": [4, 59, 168], "6k": 4, "420var": 4, "522var": 4, "2m": 4, "b": [4, 6, 25, 73, 75, 77, 78, 80, 81, 82, 168, 169, 173], "0k": 4, "891kb": 4, "270k": 4, "29mb": 4, "350k": 4, "25": [4, 8, 10, 12, 28, 29, 35, 60, 61, 63, 166, 168, 173], "11mb": 4, "03m": 4, "30mb": 4, "87m": 4, "79mb": 4, "7m": 4, "9mb": 4, "62": [4, 168], "4m": 4, "3mb": 4, "9m": 4, "5mb": 4, "4mb": 4, "finalis": 4, "26karrai": 4, "intermedi": [4, 36, 38, 45, 46, 62, 173, 174], "columnar": [4, 171, 172], "specifi": [4, 8, 17, 25, 27, 28, 29, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 58, 60, 61, 62, 63, 64, 69, 70, 166, 168, 174], "drop": [4, 6, 45, 46, 47, 54, 64, 69, 93, 169], "call_ad": 4, "third": [4, 61, 62, 63, 64, 168, 172], "unknown": [4, 6, 25, 28, 29, 57, 60, 61, 62, 63, 69, 95, 120, 168, 169, 173], "document": [4, 18, 168, 169, 170, 173, 174], "downstream": [4, 38, 46, 47, 164, 165, 166, 167], "oper": [4, 6, 49, 170], "repres": [4, 6, 45, 46, 47, 65, 74, 168, 173, 174], "where": [4, 6, 10, 21, 25, 36, 38, 45, 46, 47, 52, 61, 64, 65, 70, 165, 168, 172, 173, 174], "matrixt": 4, "load_dataset": [4, 42, 45, 50, 169, 173, 174], "ll": 4, "simplest": [4, 168, 173], "thing": 4, "lt": [4, 6], "gt": [4, 6, 173], "28mb": [4, 6], "10879": 4, "284": [4, 26], "84": 4, "coordin": [4, 6, 18, 27, 64, 66, 164, 166, 167, 168, 169, 173, 174], "int8": [4, 168, 169, 173, 174], "6mb": 4, "chunksiz": [4, 6, 168, 169, 173, 174], "10000": [4, 6, 36, 38, 45, 46, 47, 174], "meta": [4, 6, 66, 99, 168, 169, 173, 174], "ndarrai": [4, 6, 20, 24, 56, 64, 69, 168, 169, 173, 174], "call_dp": 4, "call_gq": 4, "call_genotyp": [4, 8, 10, 13, 14, 15, 17, 18, 23, 26, 30, 32, 33, 34, 45, 46, 47, 52, 59, 67, 69, 84, 163, 168, 169, 173, 174], "call_genotype_mask": [4, 14, 23, 25, 59, 80, 168, 169, 174], "bool": [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 169, 174], "call_genotype_phas": [4, 81, 174], "variant_contig": [4, 66, 70, 145, 165, 166, 167, 168, 169, 174], "11kb": [4, 168], "variant_filt": 4, "variant_id": [4, 148, 174], "87kb": 4, "variant_id_mask": [4, 174], "variant_posit": [4, 69, 158, 165, 166, 167, 168, 169, 174], "int32": [4, 174], "44kb": 4, "variant_qu": 4, "float32": [4, 37], "datasetdimens": [4, 6], "10879sampl": 4, "284allel": 4, "2ploidi": 4, "2contig": 4, "84filter": 4, "1coordin": 4, "int8dask": 4, "descript": [4, 45, 46, 47, 65, 66], "byte": [4, 6, 36, 37, 38, 39, 42, 43, 44, 45, 46, 49, 50, 53, 68, 174], "mib": [4, 6], "shape": [4, 6, 7, 9, 11, 12, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 31, 55, 56, 58, 63, 71, 72, 88, 89, 139, 140, 168, 173], "graph": [4, 6, 20, 54, 168, 173], "type": [4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 163, 164, 165, 166, 167, 168, 174], "booldask": 4, "objectdask": 4, "672": 4, "float64dask": 4, "float64": [4, 6, 66, 168, 169], "sample_id": [4, 6, 40, 41, 57, 60, 61, 62, 63, 64, 69, 102, 168, 169, 174], "22": [4, 6, 56, 146, 168, 169, 173, 174], "kib": 4, "variant_allel": [4, 45, 46, 47, 69, 142, 168, 169, 173, 174], "169": 4, "156": 4, "angl": 4, "bracket": 4, "id": [4, 6, 8, 18, 58], "point": [4, 6, 173], "assembli": 4, "statu": 4, "uniqu": [4, 6, 61, 62, 63, 79, 94, 102, 148, 173], "applic": [4, 25, 27, 36, 38, 41, 59, 70, 174], "99": [4, 168, 169], "int32dask": 4, "posit": [4, 44, 56, 63, 77, 91, 92, 158, 161, 162, 164, 165, 166, 167, 168, 174], "50": [4, 6, 24, 28, 29, 66, 168, 169, 173], "39": [4, 168, 173], "float32dask": 4, "phred": 4, "score": [4, 28, 29, 112, 159], "index": [4, 6, 8, 13, 36, 37, 39, 40, 44, 45, 46, 47, 48, 49, 51, 54, 58, 64, 78, 93, 101, 114, 145, 160, 161, 162, 164, 165, 166, 167, 168, 169, 170, 173, 174], "1vcf_header": 4, "fileformat": 4, "vcfv4": [4, 45, 46, 47, 65], "quot": 4, "hailvers": 4, "29fbaeaf265": 4, "dp": [4, 45, 46, 47], "gq": 4, "info": [4, 45, 46, 47, 65], "ac": [4, 45, 46, 47, 65, 173, 174], "af": 4, "float": [4, 14, 24, 26, 27, 28, 29, 48, 51, 52, 59, 66, 70, 74, 147, 150, 168, 174], "baseqranksum": 4, "clippingranksum": 4, "flag": [4, 26, 73, 75, 77, 78, 80, 81, 82, 168], "haplotypescor": 4, "inbreedingcoeff": 4, "mleac": 4, "mleaf": 4, "mq": 4, "mq0": 4, "mqranksum": 4, "qd": 4, "readposranksum": 4, "length": [4, 6, 36, 38, 43, 45, 46, 47, 60, 61, 62, 63, 64, 65, 69, 174], "249250621": 4, "grch37": 4, "243199373": 4, "198022430": 4, "191154276": 4, "180915260": 4, "171115067": 4, "159138663": 4, "146364022": 4, "141213431": 4, "135534747": 4, "135006516": 4, "133851895": 4, "115169878": 4, "107349540": 4, "102531392": 4, "90354753": 4, "81195210": 4, "78077248": 4, "59128983": 4, "63025520": 4, "48129895": 4, "51304566": 4, "155270560": 4, "59373566": 4, "mt": 4, "16569": 4, "gl000207": 4, "4262": 4, "gl000226": 4, "15008": 4, "gl000229": 4, "19913": 4, "gl000231": 4, "27386": 4, "gl000210": 4, "27682": 4, "gl000239": 4, "33824": 4, "gl000235": 4, "34474": 4, "gl000201": 4, "36148": 4, "gl000247": 4, "36422": 4, "gl000245": 4, "36651": 4, "gl000197": 4, "37175": 4, "gl000203": 4, "37498": 4, "gl000246": 4, "38154": 4, "gl000249": 4, "38502": 4, "gl000196": 4, "38914": 4, "gl000248": 4, "39786": 4, "gl000244": 4, "39929": 4, "gl000238": 4, "39939": 4, "gl000202": 4, "40103": 4, "gl000234": 4, "40531": 4, "gl000232": 4, "40652": 4, "gl000206": 4, "41001": 4, "gl000240": 4, "41933": 4, "gl000236": 4, "41934": 4, "gl000241": 4, "42152": 4, "gl000243": 4, "43341": 4, "gl000242": 4, "43523": 4, "gl000230": 4, "43691": 4, "gl000237": 4, "45867": 4, "gl000233": 4, "45941": 4, "gl000204": 4, "81310": 4, "gl000198": 4, "90085": 4, "gl000208": 4, "92689": 4, "gl000191": 4, "106433": 4, "gl000227": 4, "128374": 4, "gl000228": 4, "129120": 4, "gl000214": 4, "137718": 4, "gl000221": 4, "155397": 4, "gl000209": 4, "159169": 4, "gl000218": 4, "161147": 4, "gl000220": 4, "161802": 4, "gl000213": 4, "164239": 4, "gl000211": 4, "166566": 4, "gl000199": 4, "169874": 4, "gl000217": 4, "172149": 4, "gl000216": 4, "172294": 4, "gl000215": 4, "172545": 4, "gl000205": 4, "174588": 4, "gl000219": 4, "179198": 4, "gl000224": 4, "179693": 4, "gl000223": 4, "180455": 4, "gl000195": 4, "182896": 4, "gl000212": 4, "186858": 4, "gl000222": 4, "186861": 4, "gl000200": 4, "187035": 4, "gl000193": 4, "189789": 4, "gl000194": 4, "191469": 4, "gl000225": 4, "211173": 4, "gl000192": 4, "547496": 4, "chrom": [4, 48, 50], "po": [4, 26, 174], "ref": 4, "alt": [4, 173], "qual": 4, "hg00096": 4, "hg00099": 4, "hg00105": 4, "hg00118": 4, "hg00129": 4, "hg00148": 4, "hg00177": 4, "hg00182": 4, "hg00242": 4, "hg00254": 4, "hg00265": 4, "hg00271": 4, "hg00274": 4, "hg00332": 4, "hg00335": 4, "hg00369": 4, "hg00421": 4, "hg00436": 4, "hg00452": 4, "hg00472": 4, "hg00530": 4, "hg00534": 4, "hg00583": 4, "hg00590": 4, "hg00598": 4, "hg00607": 4, "hg00619": 4, "hg00623": 4, "hg00657": 4, "hg00663": 4, "hg00704": 4, "hg00705": 4, "hg00733": 4, "hg00864": 4, "hg00881": 4, "hg01052": 4, "hg01070": 4, "hg01075": 4, "hg01164": 4, "hg01174": 4, "hg01241": 4, "hg01248": 4, "hg01256": 4, "hg01275": 4, "hg01284": 4, "hg01334": 4, "hg01348": 4, "hg01396": 4, "hg01443": 4, "hg01491": 4, "hg01498": 4, "hg01537": 4, "hg01572": 4, "hg01606": 4, "hg01623": 4, "hg01630": 4, "hg01783": 4, "hg01784": 4, "hg01790": 4, "hg01799": 4, "hg01801": 4, "hg01806": 4, "hg01812": 4, "hg01813": 4, "hg01817": 4, "hg01848": 4, "hg01849": 4, "hg01857": 4, "hg01863": 4, "hg01874": 4, "hg01915": 4, "hg01924": 4, "hg01965": 4, "hg01970": 4, "hg01991": 4, "hg02010": 4, "hg02020": 4, "hg02054": 4, "hg02086": 4, "hg02087": 4, "hg02116": 4, "hg02122": 4, "hg02130": 4, "hg02131": 4, "hg02152": 4, "hg02154": 4, "hg02165": 4, "hg02224": 4, "hg02232": 4, "hg02236": 4, "hg02250": 4, "hg02259": 4, "hg02298": 4, "hg02318": 4, "hg02345": 4, "hg02351": 4, "hg02363": 4, "hg02373": 4, "hg02383": 4, "hg02384": 4, "hg02386": 4, "hg02388": 4, "hg02389": 4, "hg02397": 4, "hg02419": 4, "hg02462": 4, "hg02464": 4, "hg02497": 4, "hg02511": 4, "hg02521": 4, "hg02561": 4, "hg02574": 4, "hg02580": 4, "hg02595": 4, "hg02603": 4, "hg02629": 4, "hg02651": 4, "hg02682": 4, "hg02688": 4, "hg02690": 4, "hg02699": 4, "hg02760": 4, "hg02768": 4, "hg02771": 4, "hg02792": 4, "hg02798": 4, "hg02811": 4, "hg02814": 4, "hg02840": 4, "hg02870": 4, "hg02881": 4, "hg02970": 4, "hg02973": 4, "hg03009": 4, "hg03046": 4, "hg03074": 4, "hg03091": 4, "hg03105": 4, "hg03127": 4, "hg03193": 4, "hg03224": 4, "hg03237": 4, "hg03241": 4, "hg03247": 4, "hg03259": 4, "hg03267": 4, "hg03354": 4, "hg03366": 4, "hg03367": 4, "hg03380": 4, "hg03419": 4, "hg03449": 4, "hg03451": 4, "hg03458": 4, "hg03490": 4, "hg03491": 4, "hg03511": 4, "hg03556": 4, "hg03563": 4, "hg03598": 4, "hg03603": 4, "hg03607": 4, "hg03636": 4, "hg03684": 4, "hg03686": 4, "hg03690": 4, "hg03731": 4, "hg03740": 4, "hg03755": 4, "hg03800": 4, "hg03815": 4, "hg03832": 4, "hg03850": 4, "hg03873": 4, "hg03897": 4, "hg03905": 4, "hg03937": 4, "hg03948": 4, "hg03973": 4, "hg04054": 4, "hg04059": 4, "hg04063": 4, "hg04096": 4, "hg04099": 4, "hg04140": 4, "hg04171": 4, "hg04209": 4, "hg04210": 4, "hg04229": 4, "hg04239": 4, "na07347": 4, "na11918": 4, "na11919": 4, "na12045": 4, "na12273": 4, "na12342": 4, "na12414": 4, "na12546": 4, "na12760": 4, "na12878": 4, "na18516": 4, "na18525": 4, "na18534": 4, "na18541": 4, "na18557": 4, "na18565": 4, "na18616": 4, "na18619": 4, "na18623": 4, "na18630": 4, "na18631": 4, "na18740": 4, "na18853": 4, "na18865": 4, "na18873": 4, "na18874": 4, "na18916": 4, "na18960": 4, "na18966": 4, "na18975": 4, "na18976": 4, "na18978": 4, "na18990": 4, "na19060": 4, "na19063": 4, "na19076": 4, "na19086": 4, "na19087": 4, "na19096": 4, "na19113": 4, "na19118": 4, "na19185": 4, "na19209": 4, "na19311": 4, "na19314": 4, "na19317": 4, "na19321": 4, "na19379": 4, "na19384": 4, "na19390": 4, "na19397": 4, "na19399": 4, "na19404": 4, "na19446": 4, "na19448": 4, "na19455": 4, "na19456": 4, "na19466": 4, "na19655": 4, "na19657": 4, "na19670": 4, "na19678": 4, "na19679": 4, "na19701": 4, "na19720": 4, "na19756": 4, "na19761": 4, "na19764": 4, "na19786": 4, "na20318": 4, "na20351": 4, "na20517": 4, "na20518": 4, "na20529": 4, "na20587": 4, "na20757": 4, "na20798": 4, "na20799": 4, "na20800": 4, "na20810": 4, "na20826": 4, "na20858": 4, "na20864": 4, "na20869": 4, "na20877": 4, "na20888": 4, "na20910": 4, "na21101": 4, "na21113": 4, "na21114": 4, "na21116": 4, "na21118": 4, "na21133": 4, "na21143": 4, "vcf_zarr_vers": 4, "last": [4, 28, 29, 66, 167, 168, 173], "easili": [4, 168], "form": [4, 171, 172, 174], "variant_contig_nam": 4, "later": [4, 6, 173], "ds2": [4, 23, 64, 169], "set_index": [4, 6, 169], "max_vari": [4, 19, 168, 169], "max_sampl": [4, 19, 168], "904165": 4, "909917": 4, "986963": 4, "1563691": 4, "1707740": 4, "152660491": 4, "153031688": 4, "153674876": 4, "153706320": 4, "154087368": 4, "row": [4, 6, 19, 26, 51, 56, 61, 62, 63, 168, 169], "too": [4, 45, 46, 47, 173], "df_variant": 4, "data_var": [4, 169], "startswith": 4, "variant_": 4, "to_datafram": [4, 168], "groupbi": [4, 168], "agg": 4, "lambda": [4, 61, 62, 63, 69, 168], "head": [4, 6, 168], "five": [4, 52], "referenc": [4, 168], "dtype": [4, 6, 15, 16, 17, 18, 25, 57, 61, 62, 63, 64, 168, 169, 173, 174], "possibli": [4, 61, 62, 63], "load": [4, 6, 37, 39, 40, 45, 46, 48, 53, 65, 111, 168, 170, 173, 174], "text": [4, 6, 39, 40, 48, 50], "csv": 4, "annot": 4, "regular": [4, 24, 66], "annotations_fil": 4, "1kg_annot": 4, "df": [4, 54, 168], "read_csv": [4, 6], "sep": 4, "index_col": [4, 6], "class": 4, "core": [4, 173, 174], "frame": [4, 168], "datafram": [4, 6, 24, 51, 54, 168], "3500": 4, "entri": [4, 21], "na21144": 4, "total": [4, 25, 67, 109, 163], "null": [4, 24], "popul": [4, 6, 10, 25, 58, 61, 62, 63, 69, 132, 168, 170, 172, 173], "superpopul": 4, "isfemal": 4, "purplehair": 4, "caffeineconsumpt": 4, "int64": [4, 164, 166, 167, 168, 169, 173], "116": [4, 6, 173], "kb": 4, "gbr": 4, "eur": 4, "hg00097": 4, "hg00098": 4, "hg00100": 4, "na21137": 4, "gih": 4, "sa": 4, "na21141": 4, "na21142": 4, "join": [4, 6, 168, 173], "ds_annot": 4, "to_xarrai": 4, "renam": [4, 6, 173], "left": [4, 6, 48], "reset_index": 4, "reset_coord": 4, "2kb": [4, 66, 168, 169, 173], "x27": [4, 6], "284b": 4, "284variant": 4, "10879allel": 4, "fin": 4, "ch": 4, "pur": 4, "cdx": 4, "clm": 4, "ib": [4, 30, 129], "pel": 4, "khv": 4, "acb": 4, "gwd": 4, "pjl": 4, "esn": 4, "beb": 4, "msl": 4, "stu": 4, "itu": 4, "ceu": 4, "yri": 4, "chb": 4, "jpt": 4, "lwk": 4, "mxl": 4, "asw": 4, "tsi": 4, "ea": 4, "amr": 4, "afr": 4, "boolfals": 4, "truearrai": 4, "int644": 4, "5arrai": 4, "relev": [4, 6, 172], "seri": 4, "built": 4, "usual": [4, 6, 173], "enough": [4, 168], "ok": 4, "distribut": [4, 6, 24, 168, 170, 173, 174], "contin": 4, "to_seri": [4, 168], "value_count": 4, "1018": 4, "661": 4, "617": 4, "535": 4, "describ": [4, 6, 10, 24, 25, 27, 55, 59, 66, 168, 171, 172, 173, 174], "000000": [4, 168], "983714": 4, "std": [4, 168], "702349": 4, "min": [4, 10, 168], "75": [4, 8, 12, 60, 63, 168], "max": [4, 168], "fewer": [4, 45, 46, 47, 61, 62, 63, 168, 174], "len": 4, "72": 4, "55": [4, 63, 166, 168], "34": [4, 56, 168, 173], "415493": 4, "580549": 4, "hoc": [4, 168], "uncov": 4, "biolog": [4, 70], "insight": [4, 52], "base": [4, 6, 10, 25, 32, 33, 34, 38, 52, 54, 60, 61, 66, 97, 133, 134, 137, 166, 168, 170, 172, 173, 174], "appli": [4, 6, 25, 48, 61, 62, 63, 64, 69, 70, 168, 173], "tupl": [4, 37, 39, 40, 58, 66], "2418": 4, "2367": 4, "1929": 4, "1864": 4, "494": 4, "477": 4, "466": 4, "451": 4, "150": 4, "111": [4, 6, 146], "often": [4, 6, 168, 173], "plot": [4, 6, 168], "feel": 4, "attr": 4, "long_nam": 4, "hist": [4, 168], "rang": [4, 25, 58, 165, 170, 174], "30": [4, 56, 168, 173], "bin": [4, 168], "edgecolor": 4, "qc": 4, "process": [4, 6, 45, 46, 47, 48, 49, 54, 119, 145, 169, 170, 173, 174], "poor": 4, "iter": 4, "collect": 4, "metric": [4, 56], "equival": [4, 29, 44, 108, 110, 145, 169], "sample_qc": 4, "begin": [4, 6], "sample_": 4, "sample_n_cal": [4, 103, 169], "sample_call_r": [4, 100, 169], "sample_n_het": [4, 104, 169], "sample_n_hom_ref": [4, 106, 169], "sample_n_hom_alt": [4, 105, 169], "sample_n_non_ref": [4, 107, 169], "int64dask": 4, "rate": [4, 168], "88": 4, "sample_gq_mean": 4, "dim": [4, 6, 7, 8, 9, 12, 16, 21, 22, 25, 52, 55, 58, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 168, 173], "60": [4, 6, 19, 168], "sample_dp_mean": 4, "recent": [4, 59, 172, 173], "issu": [4, 40, 170, 172, 173], "934": 4, "scatter": [4, 6], "outlier": 4, "cutoff": 4, "sel": [4, 58, 168, 169], "print": [4, 169, 173], "remain": 4, "250": [4, 25, 168], "complic": 4, "ab": 4, "fraction": [4, 67, 100, 144, 163], "nan": [4, 6, 7, 25, 28, 29, 30, 31, 35, 55, 56, 63, 74, 130, 168, 174], "ad1": 4, "dict": [4, 6, 20, 36, 39, 43, 44, 45, 46, 47, 49, 53, 64, 65, 68, 70], "pipe": [4, 168], "adsum": 4, "Then": [4, 6, 46, 173], "condit": [4, 168], "heterozygot": 4, "balanc": 4, "hom_ref": 4, "het": 4, "hom_alt": 4, "filter_condition_ab": 4, "filter_mask": 4, "fraction_filt": 4, "2f": 4, "compar": [4, 6, 169], "time": [4, 6, 37, 39, 40, 46, 47, 173, 174], "won": [4, 174], "26mb": 4, "variant_n_cal": [4, 152, 168, 169], "variant_call_r": [4, 144, 168, 169], "variant_n_het": [4, 153, 168, 169], "variant_n_hom_ref": [4, 155, 168, 169], "variant_n_hom_alt": [4, 154, 168, 169], "variant_n_non_ref": [4, 156, 168, 169], "250b": 4, "1kb": [4, 169], "2sampl": 4, "250ploidi": 4, "variant_allele_count": [4, 9, 17, 140, 163, 168, 173], "uint64dask": 4, "With": [4, 71, 72, 88, 140, 168, 172, 173], "uint64": [4, 16, 17, 18, 168, 169, 173], "variant_allele_tot": [4, 143, 168], "variant_allele_frequ": [4, 141, 168], "restrict": [4, 173], "hardi": [4, 25, 27], "weinberg": [4, 25, 27], "equilibrium": [4, 25, 27], "tell": 4, "u": [4, 6, 71, 74, 87, 90, 94, 102, 120, 140, 145, 146, 148, 172, 173], "being": [4, 168, 173, 174], "regener": 4, "safe": 4, "u3": [4, 168, 169], "36b": [4, 169], "41": [4, 168, 173], "variant_hwe_p_valu": [4, 27, 147, 169], "variant_genotype_count": [4, 18, 27, 146, 169], "261kb": 4, "genotype_id": [4, 18, 169], "10879genotyp": 4, "3allel": 4, "p": [4, 6, 24, 25, 26, 27, 59, 66, 147, 150, 174], "hwe": [4, 27, 147], "observ": [4, 31, 48, 55, 85, 131, 146], "sort": [4, 54, 57, 63, 146], "triallel": [4, 146], "triploid": [4, 146], "000": [4, 45, 46, 47, 146], "001": [4, 146], "011": [4, 146], "002": [4, 146], "012": [4, 146], "112": [4, 29, 146], "022": [4, 146], "122": [4, 146], "222": [4, 146], "254": 4, "234": 4, "u3dask": 4, "given": [4, 6, 18, 31, 56, 168, 173, 174], "outlin": [4, 54, 63, 174], "genotypespandasindexpandasindex": 4, "1e": [4, 24, 169], "final": [4, 6, 28, 29, 38, 45, 46, 47, 65, 169, 174], "8394": 4, "linear": [4, 6, 26], "regress": [4, 25, 26, 66, 97], "trait": [4, 24, 26, 66, 139, 149, 150, 151], "ds_lr": 4, "gwas_linear_regress": 4, "add_intercept": [4, 26, 66], "covari": [4, 24, 26, 66, 89, 108], "37mb": 4, "45": [4, 25, 28, 29, 168, 173], "variant_linreg_beta": [4, 26, 149], "67kb": 4, "5439": 4, "variant_linreg_t_valu": [4, 26, 151], "variant_linreg_p_valu": [4, 26, 150], "201kb": 4, "17mb": 4, "8394trait": 4, "1genotyp": 4, "beta": [4, 6, 10, 24, 26, 122, 149, 151], "196": 4, "127": [4, 59], "48": [4, 59, 168, 173, 174], "131": [4, 61, 62, 63, 69], "32": [4, 13, 56, 69, 168, 173, 174], "37": [4, 168, 173], "doesn": [4, 173, 174], "manhattan": 4, "qq": 4, "seaborn": 4, "sn": 4, "matplotlib": [4, 6], "inlin": [4, 38], "manhattan_plot": 4, "variant_linreg_log_p_valu": 4, "log10": 4, "astyp": [4, 6, 168, 174], "overflow": 4, "cumulative_po": 4, "mojon": 4, "video_notebook": 4, "blob": 4, "master": 4, "20plot": 4, "20in": 4, "20python": 4, "ipynb": 4, "cell": [4, 173], "running_po": 4, "group_df": 4, "append": [4, 44], "concat": [4, 6], "color": [4, 173], "els": [4, 52], "relplot": 4, "hue": 4, "palett": 4, "blue": [4, 6], "orang": 4, "linewidth": 4, "legend": 4, "none": [4, 7, 8, 20, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 56, 58, 63, 65, 66, 68, 69, 70, 89, 90, 91, 92, 93, 139, 149, 151, 166, 167, 168, 174], "aspect": [4, 174], "ax": [4, 60, 108, 111, 112, 168], "set_xlabel": 4, "chromosom": [4, 39, 40, 70, 119, 168], "set_xtick": 4, "median": 4, "set_xticklabel": 4, "math": 4, "pyplot": [4, 6], "plt": [4, 6], "qq_plot": 4, "squeez": 4, "expected_p": 4, "arang": [4, 69], "observed_p": 4, "max_val": 4, "ceil": 4, "fig": 4, "subplot": 4, "figsiz": [4, 6, 168], "scatterplot": 4, "x_pred": 4, "linspac": 4, "lineplot": 4, "xlim": 4, "ylim": 4, "explain": [4, 109, 110, 168, 173], "ancestri": 4, "just": [4, 168, 173, 174], "better": [4, 38, 174], "princip": [4, 59, 108, 109, 110, 111, 112], "pca": [4, 111], "ds_pca": 4, "stat": [4, 66, 170, 173], "count_call_alternate_allel": 4, "Or": 4, "zero": [4, 6, 10, 25, 48, 51, 52, 61, 62, 63, 69, 173], "variant_mask": 4, "call_alternate_allele_count": 4, "sample_pca_project": [4, 59, 112], "453594": 4, "128805": 4, "008168": 4, "8012085": 4, "537296": 4, "0794808": 4, "496218": 4, "31961": 4, "116499": 4, "6827672": 4, "6817017": 4, "957277": 4, "873404": 4, "404314": 4, "85919": 4, "382873": 4, "368455": 4, "384331": 4, "974406": 4, "576627": 4, "124643": 4, "4210625": 4, "5393088": 4, "0124567": 4, "754401": 4, "414771": 4, "358787": 4, "7951679": 4, "4263666": 4, "985675": 4, "062882": 4, "688103": 4, "351276": 4, "205051": 4, "7339797": 4, "17502": 4, "3491": 4, "10kb": [4, 168, 169, 173], "sample_pca_compon": [4, 108], "140kb": 4, "sample_pca_explained_vari": [4, 110], "40b": [4, 168], "sample_pca_explained_variance_ratio": [4, 109], "sample_pca_load": [4, 111], "int16": 4, "2mb": 4, "7mb": 4, "250compon": 4, "10variant": 4, "3491genotyp": 4, "52": [4, 25, 168, 173], "136": 4, "int16dask": 4, "27": [4, 63, 168, 173], "81": 4, "64": [4, 29, 168], "two": [4, 6, 7, 8, 9, 12, 16, 21, 22, 31, 46, 55, 56, 58, 61, 62, 63, 69, 119, 168, 173, 174], "notic": 4, "cluster": [4, 174], "sample_pca_projection_0": 4, "sample_pca_projection_1": 4, "sample_pca_projection_2": 4, "rerun": 4, "sex": [4, 40, 41], "copi": [4, 61, 63, 70, 119, 120, 168, 173], "back": 4, "caffein": 4, "consumpt": 4, "locu": [4, 6, 18, 30, 59, 166], "clearli": 4, "appar": [4, 6], "varieti": [6, 170], "approach": [6, 28, 29], "structur": [6, 10, 20, 28, 29, 57, 60, 61, 62, 63, 64, 69, 133, 134, 135, 136, 137, 138, 170, 173], "addit": [6, 39, 43, 44, 45, 46, 47, 53, 57, 61, 62, 63, 68, 69, 70, 173, 174], "between": [6, 7, 10, 21, 25, 30, 54, 56, 58, 59, 69, 111, 114, 123, 166, 167, 168, 173, 174], "cleveland": 6, "et": [6, 7, 8, 24, 25, 26, 27, 28, 29, 59, 63, 69], "al": [6, 7, 8, 24, 25, 26, 27, 28, 29, 59, 63, 69], "2012": [6, 25, 69], "6473": 6, "3534": 6, "individu": [6, 10, 25, 26, 30, 31, 55, 59, 61, 62, 63, 66, 69, 120, 168], "across": [6, 33, 34, 66, 113, 157, 168, 173, 174], "52843": 6, "loci": [6, 69], "cleveland2012_pedigre": 6, "gz": [6, 48, 174], "cleveland2012_snps1000": 6, "inspect": 6, "commonli": [6, 40, 41, 59, 112, 173], "rcparam": 6, "figur": 6, "simpl": [6, 168, 173], "tabular": [6, 19, 168], "three": [6, 7, 8, 9, 21, 22, 27, 45, 46, 47, 55, 58, 64, 65, 168, 173], "column": [6, 19, 26, 27, 61, 62, 63, 89, 139, 168, 169], "patern": 6, "matern": 6, "while": [6, 168, 173, 174], "ped": 6, "quit": 6, "reason": [6, 173], "recommend": [6, 48, 173, 174], "sire": 6, "dam": 6, "appear": 6, "ascend": [6, 28, 54], "safer": 6, "treat": [6, 45, 46, 47, 63, 67, 163, 174], "mistaken": 6, "especi": 6, "parent_id": [6, 57, 60, 61, 62, 63, 64, 69, 94], "dataarrai": [6, 7, 8, 9, 12, 16, 21, 22, 55, 58, 168, 169, 173], "104kb": 6, "4279": 6, "6465": 6, "6466": 6, "1129": 6, "5129": 6, "6472": 6, "52kb": 6, "6471": 6, "16b": [6, 164, 168], "dataarraysampl": 6, "6473parent": 6, "samplespandasindexpandasindex": 6, "6464": 6, "6467": 6, "6468": 6, "6469": 6, "6470": 6, "parentspandasindexpandasindex": 6, "translat": 6, "likewis": 6, "primarili": [6, 70], "differenti": 6, "mani": [6, 23, 168, 172, 174], "ident": [6, 30, 31, 52, 69, 168], "207kb": 6, "2coordin": 6, "combin": [6, 18, 28, 29, 43], "typic": [6, 38, 43, 54, 168, 174], "except": [6, 21, 41, 45, 46, 47, 167, 168, 169, 174], "normal": [6, 66, 173], "re": [6, 35, 66, 173], "invalid": [6, 57, 64], "parent_indic": [6, 20, 60, 61, 62, 63, 64, 69], "4278": 6, "1128": 6, "5128": 6, "neg": [6, 24, 56, 95, 101, 166], "unkno": 6, "6463": 6, "3674": 6, "6471arrai": 6, "serv": [6, 44], "robust": 6, "record": [6, 45, 46, 47, 61, 62, 63, 173], "preserv": [6, 65, 174], "subset": [6, 28, 29, 35, 36, 61, 64, 130, 168, 170], "reorder": 6, "fast": 6, "numer": [6, 69, 120], "howev": [6, 49, 61, 69, 163, 168, 173, 174], "among": [6, 25, 28, 29, 30, 55, 63, 122, 129, 137], "simplifi": [6, 168], "assumpt": [6, 66, 170, 174], "unrel": [6, 10, 61, 62, 63], "anoth": [6, 29, 168, 173], "even": [6, 38, 60, 120, 174], "hold": [6, 8, 10, 11, 12, 13, 15, 16, 17, 18, 20, 23, 25, 26, 30, 31, 32, 33, 34, 55, 57, 59, 60, 61, 62, 63, 64, 67, 69, 163], "inaccur": 6, "varianc": [6, 24, 109, 110], "caus": [6, 35, 173], "mendelian": [6, 69], "arm": [6, 62, 63], "predigree_kinship": 6, "allow_half_found": [6, 61, 62, 63], "return_relationship": [6, 62, 63], "stat_pedigree_kinship": [6, 63, 137], "stat_pedigree_relationship": [6, 29, 35, 63, 138], "samples_0": [6, 10, 25, 28, 29, 30, 35, 59, 60, 62, 63, 64, 96, 122, 125, 126, 127, 128, 129, 130, 133, 135, 136, 137, 138], "samples_1": [6, 10, 25, 28, 29, 30, 35, 59, 60, 62, 63, 64, 96, 122, 125, 126, 127, 128, 129, 130, 133, 135, 136, 137, 138], "335mb": 6, "mul": 6, "chunktyp": [6, 168, 173], "deriv": [6, 25, 61, 63, 119, 138, 168], "6473samples_1": 6, "6473dask": 6, "319": 6, "67": [6, 168], "twice": 6, "unfortun": 6, "propag": [6, 61, 62, 63], "assign_coord": [6, 18, 58, 64, 168], "lazi": [6, 168], "think": [6, 172], "promis": 6, "immedi": 6, "evalu": [6, 28, 29, 38, 66, 168], "015625": 6, "01111412": 6, "01885986": 6, "01507568": 6, "5324707": 6, "0324707": 6, "64731": 6, "008972": 6, "02167": 6, "01508": 6, "5325": 6, "032arrai": 6, "samples_0pandasindexpandasindex": 6, "samples_1pandasindexpandasindex": 6, "matshow": 6, "attempt": [6, 170], "realiz": [6, 25], "upon": [6, 25], "share": 6, "marker": [6, 25], "construct": [6, 44, 159], "datatyp": 6, "bgen": [6, 14, 168, 172], "991": 6, "992": 6, "994": 6, "996": [6, 168], "997": [6, 168], "998": [6, 168], "999": [6, 168], "1000": [6, 36, 38, 45, 46, 47, 66, 168, 170], "584": 6, "585": 6, "587": 6, "588": 6, "589": 6, "transpos": 6, "8kb": [6, 168], "28kb": 6, "dataarrayvari": 6, "1000sampl": 6, "35341": 6, "0arrai": 6, "variantspandasindexpandasindex": 6, "590": 6, "591": 6, "592": 6, "593": 6, "594": 6, "gen": 6, "0xarrai": 6, "3534variant": 6, "1000coordin": 6, "float641": 6, "2008": [6, 25], "term": [6, 26], "m": [6, 25, 26, 28, 29, 56, 108, 110, 173], "nucleotid": [6, 168], "respect": [6, 27, 170], "purpos": [6, 48, 168, 170], "unselect": 6, "occur": [6, 38, 63, 168], "select": [6, 25, 28, 29, 51, 52, 54, 59, 64, 159, 168, 169, 172], "inbreed": [6, 61, 63, 134], "necessarili": 6, "natur": [6, 26, 174], "randomli": [6, 30, 119], "breed": [6, 25], "program": 6, "sensit": 6, "rare": 6, "initi": [6, 23, 63, 69], "naiv": [6, 168], "achiev": [6, 174], "divid": [6, 7, 8, 9, 12, 16, 21, 22, 25, 44, 52, 55, 58, 174], "sample_frequ": [6, 25], "stat_genomic_relationship": [6, 25, 29, 126], "stat_vanraden_grm_na": 6, "clariti": 6, "ancestral_frequ": [6, 25], "perfect": 6, "task": [6, 46, 47, 168, 173, 174], "long": [6, 61, 62, 63, 173, 174], "tril_idx": 6, "tril_indic": 6, "alpha": [6, 66, 97], "xlabel": 6, "ylabel": [6, 168], "tmp": [6, 174], "ipykernel_2856": 6, "892134664": 6, "futurewarn": 6, "map": [6, 36, 56, 63, 168], "whose": [6, 45, 46, 47, 65, 168], "pair": [6, 7, 10, 20, 21, 25, 30, 51, 52, 56, 59, 63, 114, 123, 133, 166, 168], "cross": 6, "progeni": [6, 69], "give": [6, 168], "wasn": 6, "alreadi": [6, 17, 26, 37, 51, 52, 61], "present": [6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 48, 50, 51, 52, 55, 58, 60, 61, 62, 63, 64, 67, 69, 163, 168, 174], "fact": 6, "bia": 6, "increas": [6, 26, 46, 47, 61, 62, 63, 119, 165, 166, 174], "obtain": [6, 174], "surrog": 6, "mcpeek": 6, "2004": 6, "unbias": 6, "Their": 6, "invers": [6, 28, 29, 35, 61, 62, 63, 69, 127, 130, 135, 136], "weight": 6, "reflect": [6, 10], "equat": 6, "hat": [6, 10, 61], "textit": 6, "interc": 6, "phi": [6, 61], "vector": [6, 56, 108], "ones": 6, "although": 6, "straightforward": [6, 174], "sub": [6, 35, 63], "invert": [6, 35], "stat_inverse_pedigree_kinship": 6, "stat_inverse_relationship": [6, 28, 35, 130], "blue_weight": 6, "blue_frequ": 6, "And": 6, "stat_vanraden_grm_blu": 6, "3477141311": 6, "2017": [6, 10, 61, 62, 63, 69], "coeffici": [6, 59, 61, 63, 96, 134], "probabl": [6, 14, 30, 31, 36, 37, 38, 59, 61, 62, 63, 83, 119, 129, 168], "approxim": [6, 25, 38, 174], "ibd": [6, 59, 61, 62, 63, 119], "descent": 6, "averag": [6, 10], "rel": [6, 10, 64], "bias": 6, "underestim": 6, "prior": 6, "knowledg": 6, "frac": [6, 10, 61], "_0": [6, 10], "rank": 6, "multi": 6, "therefor": [6, 31, 48, 61, 62, 63, 168, 174], "call_allele_frequ": [6, 30, 72], "per": [6, 7, 9, 11, 15, 16, 17, 21, 22, 31, 45, 46, 47, 55, 58, 65, 69, 173], "multipli": 6, "un": [6, 60], "stat_weir_goudet_grm": 6, "stat_weir_goudet_beta": [6, 10, 122], "uncorrect": 6, "70656024": 6, "plant": [6, 25], "anim": 6, "studi": 6, "budget": 6, "limit": [6, 27, 39, 42, 45, 50, 168, 173], "constraint": 6, "deceas": 6, "avail": [6, 7, 9, 21, 22, 38, 58, 168, 173, 174], "choos": [6, 174], "smaller": [6, 36, 45, 46, 66, 168, 169, 170, 174], "h": [6, 25, 28, 29, 127, 128], "accuraci": [6, 25], "complet": [6, 23, 76, 173, 174], "bmatrix": 6, "nan_": 6, "pad": [6, 45, 46, 47], "messier": 6, "notat": [6, 48], "gap": 6, "imag": [6, 173], "sake": 6, "genomic_sampl": [6, 28, 29], "isin": [6, 169], "earlier": 6, "a_": 6, "goal": [6, 168], "h_": 6, "factor": [6, 28, 29], "tau": [6, 28, 29, 61, 62, 63, 69], "omega": [6, 28, 29], "martini": [6, 28, 29], "2018": [6, 28, 29, 63], "fine": [6, 174], "tune": 6, "influenc": 6, "beyond": 6, "scope": 6, "along": [6, 7, 9, 21, 22, 26, 40, 48, 58, 64, 89, 139, 161, 162, 166, 168], "axi": [6, 60, 89, 139, 168], "uneven": [6, 35], "dure": [6, 168, 173, 174], "stat_vanraden_hrm_blu": 6, "pedigree_relationship": [6, 28, 29], "stat_hybrid_relationship": [6, 29, 128], "verifi": 6, "assert_array_almost_equ": 6, "loc": 6, "hickei": 6, "j": [6, 21, 25, 26, 27, 28, 29, 51, 54, 56, 59, 61, 62, 63, 66, 69, 166, 173], "forni": 6, "livestock": 6, "g3": [6, 25], "429": 6, "435": 6, "doi": 6, "1534": 6, "2fg3": 6, "001453": 6, "schrauf": [6, 28, 29], "garcia": [6, 28, 29], "baccino": [6, 28, 29], "pimentel": [6, 28, 29], "munilla": [6, 28, 29], "rogberg": 6, "mu\u00f1oz": [6, 28, 29], "cantet": [6, 28, 29], "reimer": [6, 28, 29], "gao": [6, 28, 29], "wimmer": [6, 28, 29], "simian": [6, 28, 29], "procedur": [6, 28, 29], "evolut": [6, 28, 29], "1186": 6, "s12711": 6, "018": 6, "0386": 6, "wu": 6, "ober": 6, "complex": [6, 24, 170], "biometr": 6, "359": 6, "367": 6, "1111": 6, "0006": 6, "341x": 6, "00180": 6, "predict": [6, 25, 26, 66, 97, 98, 99], "journal": [6, 25, 27, 28, 29, 59], "dairi": [6, 25, 28, 29], "scienc": [6, 25, 26, 28, 29, 172], "91": [6, 25], "4414": [6, 25], "4423": [6, 25], "3168": 6, "jd": 6, "2007": 6, "0980": 6, "unifi": [6, 10, 28, 29], "character": [6, 10], "206": [6, 10], "2085": [6, 10], "2103": [6, 10], "198424": 6, "stat_diverg": [7, 21, 123], "window_by_posit": [7, 8, 9, 21, 22, 51, 52, 55, 58, 168], "window_by_vari": [7, 8, 9, 21, 22, 51, 52, 55, 58, 168], "str": [7, 8, 20, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 58, 65, 66, 68, 168], "formula": [7, 10, 61], "hudson": 7, "1992": 7, "elabor": 7, "bhatia": 7, "2013": 7, "nei": 7, "1986": [7, 69], "tskit": 7, "hashabl": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 51, 52, 55, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 69, 163, 165, 166, 167], "diverg": [7, 123], "stat_divergence_spec": [7, 21], "otherwis": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 41, 48, 50, 55, 57, 58, 59, 60, 61, 62, 63, 66, 67, 69, 163, 164, 165, 166, 167], "behavior": [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55, 57, 58, 59, 66, 67, 69, 163, 164, 165, 166, 167, 168], "stat_fst_spec": [7, 58], "n_variant": [7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 52, 55, 57, 58, 61, 62, 63, 66, 69, 70, 164, 166, 167, 168, 169, 173], "n_sampl": [7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 23, 25, 30, 31, 46, 47, 52, 55, 57, 58, 61, 62, 63, 66, 69, 70, 164, 166, 167, 168, 169, 173], "sample_cohort": [7, 8, 9, 12, 16, 21, 22, 55, 58, 101, 168], "stat_fst": [7, 58, 114, 168], "16666667": 7, "33333333": [7, 8, 25, 61, 62], "22222222": 7, "h1": [8, 117, 118], "h12": [8, 116], "h123": [8, 115], "h2": [8, 118], "detect": [8, 24], "signatur": 8, "soft": 8, "sweep": 8, "garud": [8, 115, 116, 117, 118], "2015": [8, 26], "call_genotype_spec": [8, 13, 14, 15, 17, 18, 23, 26, 32, 33, 34, 40, 59, 65, 67, 69, 70, 163, 173], "sample_cohort_spec": [8, 16, 55], "sequenc": [8, 25, 26, 43, 44, 45, 46, 47, 49, 58, 66], "union": [8, 20, 24, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 56, 58, 64, 65, 66, 68, 69], "stat_garud_h1": [8, 117], "stat_garud_h1_spec": 8, "stat_garud_h12": [8, 116], "stat_garud_h12_spec": 8, "stat_garud_h123": [8, 115], "stat_garud_h123_spec": 8, "stat_garud_h2_h1": [8, 118], "stat_garud_h2_h1_spec": 8, "notimplementederror": [8, 27, 60, 69], "valueerror": [8, 13, 18, 25, 27, 28, 29, 40, 41, 44, 51, 52, 54, 57, 59, 60, 61, 62, 63, 66, 67, 69, 163, 166, 173], "375": [8, 21, 60, 63], "625": [8, 21, 28, 29, 35, 60, 63], "stat_divers": [9, 22, 124, 168], "tajima": [9, 121, 124], "variant_allele_count_spec": [9, 17, 163], "divers": [9, 21, 124, 168], "stat_diversity_spec": [9, 22], "stat_tajimas_d_spec": 9, "stat_tajimas_d": [9, 121], "88883234": 9, "18459998": 9, "40517586": 9, "10393559": 9, "stat_identity_by_st": [10, 30, 129], "weir": [10, 59, 63, 122], "goudet": [10, 63, 122], "diagon": [10, 24, 51, 61, 63, 125, 133, 137], "self": [10, 59, 61, 63, 125, 137], "accur": 10, "stat_identity_by_state_spec": [10, 30], "stat_weir_goudet_beta_spec": 10, "n_allel": [10, 13, 69, 70], "seed": [10, 11, 13, 15, 17, 18, 23, 25, 30, 31, 57, 61, 62, 63, 66, 69, 70, 168, 173], "inherit": [10, 69, 119, 120, 174], "s0": [10, 11, 12, 13, 15, 16, 17, 18, 23, 30, 31, 57, 60, 61, 62, 63, 64, 69, 168, 169, 173], "s1": [10, 11, 12, 13, 15, 16, 17, 18, 23, 30, 31, 57, 60, 61, 62, 63, 64, 69, 168, 169, 173], "s2": [10, 12, 16, 30, 57, 60, 61, 62, 63, 64, 69, 168, 169, 173], "beta0": 10, "beta_correct": 10, "bruce": [10, 59, 63, 69], "j\u00e9r\u00f4me": [10, 63], "related": [10, 25, 59], "call_allele_count": [11, 15, 16, 17, 25, 31, 71, 173], "frequenc": [11, 12, 25, 30, 51, 52, 59, 72, 88, 141, 163, 168], "call_allele_count_spec": [11, 15, 16, 17, 31, 173], "count_call_allel": [11, 16, 17, 25, 31, 173], "call_allele_frequency_spec": [11, 30], "cohort_allele_count": [12, 16, 21, 22, 87], "cohort_allele_count_spec": [12, 16, 21, 22], "count_cohort_allel": [12, 21, 22], "cohort_allele_frequency_spec": 12, "s3": [12, 16, 60, 61, 62, 63, 64, 69, 168, 169, 173, 174], "call_genotype_index_spec": [13, 173], "call_genotype_index_mask_spec": 13, "missing_pct": [13, 23, 25, 70, 168, 169, 173], "call_genotype_index": [13, 79, 173], "call_genotype_prob": [14, 83], "threshold": [14, 51, 52], "hard": 14, "read_bgen": [14, 36, 38, 173], "call_genotype_probability_spec": [14, 37], "met": 14, "exceed": 14, "mask": [14, 36, 38, 59, 168], "call_genotype_mask_spec": [14, 40, 59, 65, 69, 70], "uint8": [15, 25, 36, 38, 173], "argument": [17, 23, 29, 53, 56, 68, 168, 173, 174], "liter": [17, 25, 28, 29, 30, 56, 60, 61, 62, 63, 69], "multiset": 18, "cardin": 18, "manner": 19, "denot": [19, 56], "separ": [19, 46, 66, 139, 168, 173, 174], "genotype_phas": 19, "unphas": [19, 70, 81], "maximum": [19, 41, 45, 46, 47, 59, 64, 173, 174], "tabl": 19, "truncat": [19, 45, 46, 47], "genotypedisplai": 19, "printabl": 19, "graph_attr": 20, "node_attr": [20, 173], "edge_attr": 20, "direct": [20, 63], "acycl": 20, "parent_spec": [20, 57, 60, 61, 62, 63, 64, 69, 119, 120], "through": [20, 26, 37, 39, 40, 49, 66, 168, 170], "node": [20, 173], "broadcast": 20, "edg": 20, "runtimeerror": 20, "instal": [20, 170], "digraph": 20, "66666667": [21, 22, 25, 62], "83333333": [21, 22], "partial": [23, 25, 67, 76, 163], "call_genotype_complete_spec": 23, "call_genotype_complete_mask_spec": 23, "call_genotype_complet": [23, 76], "call_genotype_complete_mask": [23, 75], "overwrit": [23, 173], "explicitli": [23, 27, 168], "futher": 23, "ld": [24, 51, 52, 54, 93, 159], "reg_covar": 24, "cheng": 24, "2020": [24, 25, 48, 66, 172], "ol": [24, 26], "2d": [24, 26, 66, 89, 139], "gaussianmixtur": 24, "unlik": [24, 168], "alwai": [24, 51, 52, 133, 168], "second": [24, 26, 30, 46, 64, 84, 89, 139, 168, 174], "mixtur": [24, 67, 163, 168], "largest": 24, "compos": 24, "test_q": 24, "q_var": 24, "pval": 24, "ramachandran": 24, "l": [24, 25, 28, 29, 66, 69], "crawford": 24, "enabl": [24, 173, 174], "enrich": 24, "underli": [24, 168, 174], "plo": 24, "e1008855": 24, "lab": 24, "aka": [25, 28, 29], "grm": [25, 126], "autopolyploid": [25, 61, 62, 63, 67, 69, 163], "ashraf": 25, "2016": [25, 59], "bilton": 25, "shrinkag": 25, "jannick": 25, "aim": 25, "densiti": [25, 51, 52], "ancestr": 25, "under": [25, 169], "infer": [25, 26, 32, 33, 34], "stat_genomic_relationship_spec": [25, 29], "cannot": [25, 26, 37, 39, 40, 41, 42, 173], "incorrect": 25, "depend": [25, 26, 38, 173, 174], "monomorph": 25, "rrblup": 25, "93617021": 25, "21276596": 25, "72340426": 25, "17021277": 25, "04255319": 25, "68085106": 25, "9744836": 25, "16978417": 25, "58417266": 25, "33778858": 25, "45323741": 25, "47619048": 25, "89496403": 25, "62446043": 25, "34820144": 25, "79951397": 25, "imput": [25, 74], "call_dosage_imput": 25, "14337789": 25, "49331713": 25, "2272175": 25, "32806804": 25, "75577157": 25, "527339": 25, "29404617": 25, "byrn": 25, "f\u00e9": 25, "czaban": 25, "asp": 25, "pedersen": 25, "lenk": 25, "roulund": 25, "didion": 25, "jensen": 25, "janss": 25, "herit": [25, 66], "famili": [25, 40, 41, 59], "pool": 25, "perenni": 25, "ryegrass": 25, "theoret": [25, 61, 62, 63, 69], "129": 25, "develop": [25, 170, 172, 173], "phd": 25, "thesi": 25, "univers": 25, "otago": 25, "1405": 25, "1413": 25, "ridg": [25, 66, 97], "kernel": 25, "255": 25, "continu": [26, 66, 139], "solv": 26, "simultan": 26, "facilit": [26, 168], "orthogon": [26, 66], "phenotyp": [26, 28, 29, 40, 41, 139], "consequ": 26, "rotat": [26, 173], "signific": 26, "independ": [26, 52, 54], "1d": [26, 66, 139], "covariates_spec": [26, 66], "traits_spec": [26, 66], "intercept": [26, 66], "valid": [26, 173], "parameter": 26, "free": [26, 59, 168], "block": [26, 37, 39, 40, 66, 97, 98], "tall": 26, "skinni": 26, "num": [26, 27, 59, 66], "hasti": 26, "trevor": 26, "robert": 26, "tibshirani": 26, "jerom": 26, "friedman": 26, "2009": [26, 28, 29], "element": [26, 36, 38, 130, 133], "mine": 26, "springer": 26, "busi": 26, "media": 26, "loh": 26, "ru": 26, "georg": 26, "tucker": 26, "brendan": 26, "k": 26, "bulik": 26, "sullivan": 26, "bjarni": 26, "vilhj\u00e1lmsson": 26, "hilari": 26, "finucan": 26, "rani": 26, "salem": 26, "daniel": 26, "chasman": 26, "bayesian": 26, "model": [26, 59, 66, 168, 172], "power": [26, 168], "exact": 27, "wigginton": 27, "2005": 27, "precomput": 27, "keyerror": [27, 57], "jani": 27, "david": 27, "cutler": 27, "goncalo": 27, "abecasi": 27, "american": [27, 59], "human": [27, 59], "887": 27, "genomic_inverse_relationship": 28, "pedigree_inverse_relationship": 28, "pedigree_subset_inverse_relationship": [28, 29], "hybrid": [28, 29, 127, 128], "hrm": [28, 29], "stat_inverse_relationship_spec": [28, 29, 35], "stat_pedigree_inverse_relationship_spec": [28, 29, 62], "boolean": [28, 29, 35, 64, 168], "absent": [28, 29, 66, 98], "expand": [28, 29], "legarra": [28, 29], "aguil": [28, 29], "2010": [28, 29], "stat_hybrid_inverse_relationship_spec": 28, "125": [28, 29, 35, 63], "subset_sampl": [28, 35], "stat_hybrid_inverse_relationship": [28, 127], "round": [28, 29, 35, 48], "987": 28, "332": 28, "549": 28, "574": 28, "247": 28, "roberg": [28, 29], "aguilar": [28, 29], "misztal": [28, 29], "4656": [28, 29], "4663": [28, 29], "johnson": [28, 29], "tsuruta": [28, 29], "lawlor": [28, 29], "holstein": [28, 29], "743": [28, 29], "752": [28, 29], "stat_pedigree_relationship_spec": [29, 63], "stat_hybrid_relationship_spec": 29, "adjac": 29, "084": 29, "056": 29, "028": 29, "653": 29, "013": 29, "576": 29, "drawn": [30, 31], "random": [30, 31, 59, 66, 69, 70], "multipl": [30, 37, 39, 40, 43, 45, 46, 47, 49, 61, 62, 63, 69, 166, 170, 173], "heterozygos": [31, 55, 67, 85, 131, 163], "polyploid": [31, 170], "haploid": 31, "call_heterozygosity_spec": [31, 55], "call_heterozygos": [31, 55, 85], "call_genotype_fil": [32, 77], "call_genotype_fill_spec": [32, 69], "call_ploidy_spec": [32, 33, 34], "call_ploidi": [33, 34, 86], "infer_call_ploidi": [33, 34], "sample_ploidy_spec": 33, "variant_ploidy_spec": 34, "subset_rechunk": 35, "567": 35, "233": 35, "region": [36, 44, 45, 46, 47, 48, 49, 174], "chunk_width": [36, 38, 45, 46, 47, 174], "compressor": [36, 38, 45, 46, 47, 48, 174], "blosc": [36, 38, 45, 46, 47], "cname": [36, 38, 45, 46, 47], "zstd": [36, 38, 45, 46, 47], "clevel": [36, 38, 45, 46, 47], "shuffl": [36, 38, 45, 46, 47], "bitshuffl": [36, 38], "blocksiz": [36, 38, 45, 46, 47, 168], "probability_dtyp": [36, 38], "max_mem": [36, 38], "4gb": [36, 38], "pack": [36, 38], "tempdir": [36, 38, 45, 46, 174], "rechunk_bgen": 36, "mutablemap": [36, 38, 39, 42, 43, 46, 50, 53, 68], "system": [36, 38, 39, 42, 43, 45, 46, 50, 53, 68, 174], "slice": [36, 165, 168, 169], "isel": [36, 168], "semant": [36, 168], "10_000": [36, 38], "width": [36, 38, 45, 46, 47, 174], "1_000": [36, 38], "raw": 36, "vertic": [36, 54], "horizont": 36, "target": [36, 174], "No": [36, 45, 46, 47, 52], "either": [36, 38, 39, 40, 41, 42, 44, 48, 56, 61, 62, 63, 168, 173, 174], "uint16": [36, 38], "loss": [36, 38], "precis": [36, 38, 48, 174], "alter": [36, 38, 57], "amount": [36, 38, 173], "worker": [36, 38, 173, 174], "100mb": [36, 38, 44], "optim": [36, 38, 48], "unnecessari": [36, 38], "collaps": [36, 38], "restor": [36, 38], "expens": [36, 38, 68, 173], "extra": [36, 38, 45, 46, 47, 65, 173, 174], "temporari": [36, 38, 45, 46, 174], "bi": [36, 37, 38], "metafile_path": 37, "sample_path": 37, "lock": [37, 39, 40], "persist": [37, 39, 40], "contig_dtyp": 37, "gp_dtype": 37, "companion": [37, 168], "offset": [37, 166, 174], "metafil": 37, "slower": [37, 39, 40], "subsequ": 37, "fetch": 37, "prefer": 37, "embed": 37, "synchron": [37, 39, 40], "concurr": [37, 39, 40], "from_arrai": [37, 39, 40], "latest": [37, 38, 39, 40, 66], "consider": [37, 39, 40, 174], "metadata": [37, 173, 174], "variant_id_spec": [37, 40, 65], "variant_contig_spec": [37, 40, 65, 66, 70, 165, 166, 167], "variant_position_spec": [37, 40, 65, 70, 165, 166], "variant_allele_spec": [37, 40, 65, 70], "sample_id_spec": [37, 40, 57, 64, 65, 70, 94], "call_dosage_mask_spec": 37, "call_genotype_probability_mask_spec": 37, "origin": [38, 48, 61, 62, 63, 111, 168, 170], "experi": 38, "larger": [38, 45, 46, 47, 65, 168, 173], "fairli": 38, "aggress": 38, "lazili": [38, 168], "slow": [38, 46], "serial": 38, "bed_path": [39, 40, 41, 42], "bim_path": [39, 40, 41, 42], "fam_path": [39, 40, 41, 42], "fam_sep": [39, 40], "bim_sep": [39, 40], "bim_int_contig": [39, 40], "storage_opt": [39, 43, 44, 53, 68, 174], "suffix": [39, 40, 41, 42, 44], "bed": [39, 40, 41, 42, 173], "fam": [39, 40, 41, 42, 173], "bim": [39, 40, 41, 42, 173], "intern": [39, 40, 41, 42, 168, 173], "conjunct": [39, 40, 41, 42, 168], "delimit": [39, 40], "interpret": [39, 40, 70, 111, 120], "encount": [39, 40, 174], "plain": [39, 40], "lead": [39, 40], "upward": [39, 40], "10x": [39, 40], "backend": [39, 43, 44, 45, 46, 47, 53, 68, 168, 174], "fsspec": [39, 43, 44, 45, 46, 47, 53, 68, 174], "a1": 40, "a2": 40, "someth": [40, 51, 52, 168, 173], "www": [40, 66], "cog": 40, "ax_allel": 40, "dimension": [40, 56], "accompani": 40, "sample_family_id": [40, 41], "fid": [40, 41], "sample_member_id": [40, 41], "sample_paternal_id": [40, 41], "father": [40, 41, 59], "sample_maternal_id": [40, 41], "mother": [40, 41, 59], "sample_sex": [40, 41], "code": [40, 41, 168, 170, 173, 174], "male": [40, 41], "femal": [40, 41], "sample_phenotyp": [40, 41], "taken": 41, "url": [43, 47, 174], "concaten": [43, 46, 89, 139, 174], "vcf_path": 44, "index_path": 44, "num_part": [44, 174], "target_part_s": [44, 45, 46, 49, 174], "partit": [44, 70, 170], "bcf": [44, 45, 46, 47, 49, 174], "csi": [44, 45, 46, 47, 49, 174], "bgzf": 44, "boundari": 44, "desir": [44, 45, 46, 47, 49, 66, 173, 174], "abbrevi": 44, "100_000_000": 44, "neither": 44, "autoshuffl": [45, 46, 47], "tempdir_storage_opt": [45, 46], "mixed_ploidi": [45, 46, 47, 168, 174], "truncate_cal": [45, 46, 47, 174], "max_alt_allel": [45, 46, 47], "exclude_field": [45, 46, 47], "field_def": [45, 46, 47, 65, 174], "delet": [45, 46], "pick": [45, 46, 49], "sequenti": [45, 46, 48, 49, 174], "extract": [45, 46, 47, 49, 168, 173], "prioriti": [45, 46, 49, 173], "nest": [45, 46, 47], "dictionari": [45, 46, 47, 65, 70, 169], "overrid": [45, 46, 47, 65, 174], "basi": [45, 46, 47], "evenli": [45, 46, 174], "divis": [45, 46], "sentinel": [45, 46, 47, 168], "incomplet": [45, 46, 47, 174], "prefix": [45, 46, 47], "wildcard": [45, 46, 47], "permit": [45, 46, 47], "definit": [45, 46, 47, 65, 170], "hq": [45, 46, 47, 65], "haplotyp": [45, 46, 47, 65], "spec": [45, 46, 47, 65], "samtool": [45, 46, 47, 65], "ht": [45, 46, 47, 65], "pdf": [45, 46, 47, 65], "carri": [46, 49], "concat_zarr": [46, 174], "lower": [46, 47, 77, 174], "cost": [46, 47, 173], "becom": [46, 47], "ratio": [46, 47, 109, 168], "proport": [46, 47, 133], "n_ploidi": [46, 47, 61, 62, 63, 70, 168], "mainli": [46, 47], "chunk_siz": [46, 47], "retain": 46, "output_storage_opt": 47, "decreas": 47, "dictat": 48, "decim": [48, 174], "expon": 48, "5e": 48, "throughput": 48, "speed": [48, 174], "mb": [48, 173], "appl": 48, "m1": 48, "accord": 48, "onc": [48, 168, 173], "post": 48, "extern": 48, "bgzip": [48, 174], "bcftool": [48, 174], "tabix": [48, 174], "sy": 48, "stdout": 48, "textio": [48, 50], "scratch": [48, 50], "variant_scor": [51, 52, 159], "spars": [51, 52, 54], "linkag": [51, 52, 69], "disequilibrium": [51, 52], "roger": 51, "huff": 51, "r2": [51, 52, 54], "exce": [51, 69, 174], "below": [51, 52, 168], "almost": [51, 52, 168], "priorit": [51, 52, 159], "variant_score_spec": [51, 52], "upper": 51, "triangl": 51, "coo": 51, "cmp": 51, "prune": [52, 93], "maxim": [52, 54], "mi": 52, "maximal_independent_set": 52, "comparison": [52, 56], "anyth": 52, "pruned_d": 52, "kwarg": [53, 66, 68, 173], "thin": [53, 68], "wrapper": [53, 68, 174], "open_zarr": [53, 173], "sensibl": [53, 68], "pipelin": [53, 68, 168], "impli": 54, "discuss": [54, 169, 170, 172], "ld_prune_index_to_drop_spec": 54, "individual_heterozygos": 55, "stat_observed_heterozygosity_spec": 55, "intev": 55, "stat_observed_heterozygos": [55, 131], "euclidean": 56, "split_everi": 56, "devic": 56, "distanc": [56, 166, 167], "illustr": [56, 168, 173], "let": [56, 173], "v0": 56, "v1": 56, "v2": 56, "v3": 56, "symmetr": 56, "vi": 56, "vj": 56, "correl": [56, 111], "depth": [56, 64], "recurs": 56, "aggreg": [56, 168, 173], "reduct": [56, 66, 97], "heurist": 56, "global": 56, "architectur": 56, "ith": 56, "jth": 56, "da": 56, "44948974": 56, "69041576": 56, "47722558": 56, "44089210e": 56, "62956526e": 56, "82353505e": 56, "00000000e": 56, "14285714e": 56, "parent_id_spec": [57, 64], "u2": [57, 61, 62, 63, 64, 168, 169], "tripl": [58, 132], "fst": [58, 114, 168], "stat_pbs_spec": 58, "n_cohort": 58, "cohort_nam": [58, 168], "co_": 58, "cohorts_0": [58, 114, 123, 132, 168], "cohorts_1": [58, 114, 123, 132, 168], "cohorts_2": [58, 132], "stat_pb": [58, 132], "co_0": 58, "co_1": 58, "co_2": 58, "160898": 58, "maf": 59, "sample_pc": 59, "pc": [59, 96, 112], "conomo": 59, "sister": 59, "brother": 59, "daughter": 59, "son": 59, "grandmoth": 59, "grandfath": 59, "granddaught": 59, "grandson": 59, "aunt": 59, "uncl": 59, "niec": 59, "nephew": 59, "cousin": 59, "half": [59, 61, 62, 63, 69, 166], "sxvxd": 59, "sxpc": 59, "sample_pca_projection_spec": 59, "genesi": 59, "pc_relate_phi_spec": 59, "arraylik": 59, "matthew": [59, 61, 62, 63, 69], "alexand": 59, "reiner": 59, "timothi": 59, "thornton": 59, "stat_hamilton_kerr_tau": [60, 61, 62, 63, 69, 120], "contribut": [60, 61, 62, 63, 69, 120, 133, 170], "manipul": [60, 168], "clonal": [60, 61, 62, 63], "reproduct": [60, 61, 62, 63, 69, 120], "stat_hamilton_kerr_tau_spec": [60, 61, 62, 63, 69, 119], "stat_pedigree_contribution_spec": 60, "odd": 60, "s4": [60, 64, 69, 169, 173], "s5": [60, 169, 173], "stat_pedigree_contribut": [60, 133], "stat_hamilton_kerr_lambda": [61, 62, 63, 69, 119], "hamilton": [61, 62, 63, 69], "kerr": [61, 62, 63, 69], "suitabl": [61, 62, 63, 69, 169, 173], "sexual": [61, 62, 63, 69, 120], "stat_hamilton_kerr_lambda_spec": [61, 62, 63, 69, 120], "unrecord": [61, 62, 63, 69], "gamet": [61, 62, 63, 120], "stat_pedigree_inbreeding_spec": 61, "minim": 61, "_i": 61, "_": 61, "ii": 61, "k_i": 61, "greater": [61, 62, 63], "inbr": [61, 62, 63], "stat_pedigree_inbreed": [61, 134], "somat": [61, 63], "unreduc": [61, 62, 63], "tetraploid": [61, 62, 63, 174], "07222222": 61, "homologu": [61, 63, 119], "richard": [61, 62, 63, 69], "851": [61, 62, 63, 69], "860": [61, 62, 63, 69], "stat_pedigree_inverse_kinship_spec": 62, "stat_pedigree_inverse_kinship": [62, 135], "stat_pedigree_inverse_relationship": [62, 136], "40112994": 62, "06779661": 62, "stat_genomic_kinship_spec": 63, "stat_pedigree_kinship_spec": 63, "loop": 63, "inconsist": 63, "topolog": 63, "children": [63, 64], "oppos": 63, "225": 63, "425": 63, "30416667": 63, "toma": 63, "kai": 63, "molecular": 63, "ecologi": 63, "4121": 63, "4135": 63, "ancestor_depth": 64, "descendant_depth": 64, "sel_samples_0": 64, "sel_samples_1": 64, "update_parent_id": 64, "drop_par": 64, "inclus": [64, 91, 165, 174], "ancestor": 64, "descend": 64, "ds1": 64, "ds3": 64, "call_genotype_phased_spec": [65, 70], "variant_block_s": 66, "sample_block_s": 66, "transform": [66, 174], "techniqu": 66, "subtract": 66, "residu": 66, "preprint": 66, "simpler": [66, 170], "technic": 66, "overview": [66, 170], "stage": [66, 97, 98, 99], "involv": [66, 174], "defini": 66, "whichev": 66, "split": [66, 174], "datas": 66, "apriori": 66, "rescal": 66, "stdev": 66, "experiment": 66, "binari": 66, "yet": 66, "outcom": [66, 97, 98, 99], "regenie_base_predict": [66, 97], "regenie_base_prediction_spec": 66, "regenie_meta_predict": [66, 99], "train": [66, 99], "regenie_meta_prediction_spec": 66, "regenie_loco_predict": [66, 98], "loco": [66, 98], "held": [66, 98], "regenie_loco_prediction_spec": 66, "n_contig": [66, 70, 164, 166, 167, 168, 169], "n_covari": 66, "n_trait": 66, "randomst": 66, "sample_covari": 66, "sample_trait": 66, "26kb": [66, 169], "20kb": 66, "4588": 66, "3734": 66, "4kb": [66, 168], "4886": 66, "mbatchou": 66, "barnard": 66, "backman": 66, "marcketta": 66, "computation": 66, "quantit": [66, 168, 170], "biorxiv": 66, "1101": 66, "162354v2": 66, "abstract": 66, "glow": 66, "tertiari": 66, "qualiti": [67, 163, 172], "sample_n_called_spec": 67, "sample_call_rate_spec": 67, "sample_n_het_spec": 67, "sample_n_hom_ref_spec": 67, "sample_n_hom_alt_spec": 67, "sample_n_non_ref_spec": 67, "fulli": [67, 163], "classifi": [67, 163], "to_zarr": 68, "uniform": 68, "simul": [69, 70, 173], "maccluer": 69, "throughout": [69, 174], "initialis": 69, "unsign": [69, 174], "bit": [69, 170, 174], "pattern": 69, "reshap": 69, "sim": 69, "uint32": 69, "jean": 69, "john": 69, "vanderberg": 69, "oliv": 69, "ryder": 69, "zoo": 69, "biologi": 69, "147": 69, "160": 69, "li": 69, "tier": 69, "gregori": 69, "dutkowski": 69, "thoma": 69, "mcrae": 69, "speci": 69, "1271": 69, "1282": 69, "meaningless": 70, "quantiti": [70, 74, 168], "interest": 70, "overwritten": 70, "appropri": [70, 169, 173], "context": [70, 108, 168], "percentag": 70, "field_nam": 70, "field_dtyp": 70, "arraylikespec": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "default_nam": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "__doc__": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "nallel": [71, 72], "ncorrespond": [71, 72, 88, 139, 140], "kind": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 168], "ndim": [71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "call_dosage_mask": 73, "ndosag": 74, "recess": 74, "domin": 74, "probabilist": 74, "ncall": [76, 84], "ncomplet": 76, "na": [77, 78, 81, 101, 130], "nindic": [77, 79, 95], "call_genotype_index_mask": 78, "nto": [78, 79, 110], "nsingl": 79, "nfor": 79, "nall": 81, "call_genotype_probability_mask": 82, "nthe": [84, 99, 108, 119, 130, 146], "nmiss": 84, "nobserv": [85, 131], "cohort_allele_frequ": 88, "ncohort": 88, "ncovari": 89, "nvariabl": 89, "nwill": 89, "interval_contig_nam": [90, 165], "interval_start": [91, 165], "interval_stop": [92, 165], "stop": [92, 162, 164, 165, 166, 167], "exclus": [92, 165], "ld_prune_index_to_drop": 93, "nvariant": [93, 140], "nuniqu": 94, "pc_relate_phi": 96, "nregeni": [97, 98, 99], "npredict": 97, "regeni": [97, 98, 99, 172], "nresult": 98, "nheld": 98, "nat": 98, "belong": 101, "member": 101, "eigenvector": 108, "nin": 108, "svd": 108, "right": 108, "decomposit": [108, 109, 110], "dask_ml": [108, 109, 110], "truncatedsvd": [108, 109, 110], "components_": 108, "ni": [109, 110], "explained_variance_ratio_": 109, "eigenvalu": [110, 111], "eigendecomposit": 110, "explained_variance_": 110, "squar": 111, "root": 111, "nthese": 111, "nand": [111, 139], "onto": 112, "nrefer": 112, "simpli": [112, 173, 174], "sample_ploidi": 113, "nwith": [113, 137, 157], "fixat": 114, "chosen": 119, "nfrom": 119, "nthi": 119, "nmeiotic": 119, "asexu": [119, 120], "nsee": [119, 120], "meiotic": 119, "nnumer": 120, "nploidi": 120, "nsexual": 120, "broadli": [120, 173], "nasexu": 120, "nare": 120, "nmatch": 120, "pi": 124, "stat_genomic_kinship": 125, "ngenom": [125, 126], "npairwis": [129, 137], "outsid": 130, "nexpect": 133, "nbase": 133, "asymmetr": 133, "nelement": 133, "ndiagon": 133, "ntrait": 139, "n2d": 139, "nindex": 145, "nscenario": [145, 169], "ngener": [145, 169], "scenario": 145, "ncount": 146, "variant_ploidi": 157, "nscore": 159, "window_contig": [160, 166, 167], "window_start": [161, 164, 166, 167], "window_stop": [162, 164, 166, 167], "variant_n_called_spec": 163, "variant_call_rate_spec": 163, "variant_n_het_spec": 163, "variant_n_hom_ref_spec": 163, "variant_n_hom_alt_spec": 163, "variant_n_non_ref_spec": 163, "variant_allele_total_spec": 163, "variant_allele_frequency_spec": 163, "span": [164, 165, 166, 167, 168], "window_start_spec": [164, 165, 166, 167], "window_stop_spec": [164, 165, 166, 167], "8b": [164, 168], "act": 165, "never": [165, 166, 167], "monoton": [165, 166, 174], "interval_contig_name_spec": 165, "interval_start_spec": 165, "interval_stop_spec": 165, "window_contig_spec": [165, 166, 167], "window_start_posit": 166, "center": [166, 168], "shift": 166, "contigu": [166, 167, 168, 174], "ds_w1": 166, "192b": 166, "64b": 166, "zip": 166, "ds_w2": 166, "240b": 166, "80b": [166, 168, 173], "96b": 167, "32b": 167, "overlap": 167, "144b": 167, "48b": 167, "toolkit": 168, "advantag": [168, 174], "ecosystem": [168, 170], "cupi": [168, 173], "interfac": 168, "cuda": 168, "fit": [168, 174], "aid": 168, "workflow": [168, 170], "assai": 168, "express": 168, "might": [168, 172, 173], "visual": 168, "1mb": 168, "184b": [168, 169], "u4": 168, "s248": 168, "s249": 168, "500kb": 168, "presenc": 168, "snv": 168, "shown": [168, 173], "entir": [168, 174], "884b": 168, "20b": 168, "120b": 168, "s7": [168, 169, 173], "s8": [168, 169], "s9": [168, 169], "200b": [168, 169, 173], "18b": 168, "referen": 168, "allele_index": 168, "2b": 168, "item": 168, "summar": 168, "variou": [168, 174], "well": [168, 172, 173, 174], "integr": 168, "domain": [168, 170], "logic": 168, "s246": 168, "s247": 168, "flexibl": [168, 174], "come": 168, "abl": 168, "transit": 168, "unstack": 168, "fillna": 168, "call_rat": 168, "898": 168, "910": 168, "894": 168, "892": 168, "906": 168, "900": 168, "titl": 168, "allud": 168, "further": 168, "nearli": 168, "9kb": 168, "800b": [168, 169], "transpar": 168, "isn": 168, "workaround": [168, 174], "design": [168, 170, 172], "own": [168, 173, 174], "accomplish": 168, "analys": [168, 172], "help": [168, 174], "exploratori": 168, "advanc": 168, "ever": 168, "worri": [168, 174], "high": 168, "locat": 168, "is_heterozyg": 168, "4b": 168, "lone": 168, "aren": 168, "realli": 168, "awar": 168, "ten": 168, "africa": 168, "asia": 168, "europ": 168, "00823045": 168, "02510823": 168, "04372041": 168, "12240725": 168, "11305475": 168, "readabl": 168, "introduc": [168, 171], "accident": 168, "namespac": 168, "collis": 168, "idiom": 168, "57": 168, "ds_qc": 168, "drop_dim": 168, "u1": [168, 174], "804800": 168, "063125": 168, "560000": 168, "780000": 168, "800000": 168, "840000": 168, "960000": 168, "00091611": 168, "00588756": 168, "00550994": 168, "blockwis": 168, "interchang": 168, "freeli": 168, "notabl": [168, 174], "actual": 168, "until": 168, "retriev": 168, "client": [168, 173, 174], "coerc": 168, "asarrai": 168, "22kb": [168, 173], "600b": [168, 169], "unbox": 168, "69": 168, "real": 168, "unchunk": 168, "leav": 168, "trade": [168, 174], "modifi": 168, "regardless": 168, "delai": [168, 173, 174], "23kb": 169, "s47": 169, "s48": 169, "s49": 169, "s45": 169, "s46": 169, "drop_var": 169, "21kb": 169, "24b": 169, "multiindex": 169, "6b": 169, "300b": 169, "658": 169, "s6": [169, 173], "s10": 169, "s11": 169, "s12": 169, "s13": 169, "s14": 169, "s15": 169, "s16": 169, "s17": 169, "s18": 169, "s19": 169, "s20": 169, "s21": 169, "s22": 169, "s23": 169, "s24": 169, "s25": 169, "s26": 169, "s27": 169, "s28": 169, "s29": 169, "s30": 169, "s31": 169, "s32": 169, "s33": 169, "s34": 169, "s35": 169, "s36": 169, "s37": 169, "s38": 169, "s39": 169, "s40": 169, "s41": 169, "s42": 169, "s43": 169, "s44": 169, "3kb": 169, "400b": 169, "pos0": 169, "32kb": [169, 173], "792b": 169, "198b": 169, "old": 169, "analyt": 170, "framework": 170, "intend": 170, "adopt": 170, "broader": 170, "easi": 170, "down": [170, 173], "done": [170, 173, 174], "front": 170, "inspir": 170, "heavili": 170, "popular": [170, 172], "focu": 170, "chain": 170, "guid": 170, "deploy": 170, "troubleshoot": 170, "highlight": 170, "cloud": 170, "forum": 170, "repositori": 170, "review": 170, "changelog": 170, "unreleas": 170, "june": 170, "2024": 170, "2023": 170, "februari": 170, "search": 170, "2022": 171, "team": [171, 172], "announc": [171, 172], "oxford": 172, "began": 172, "collabor": 172, "earli": 172, "successor": 172, "ve": 172, "close": 172, "parti": 172, "author": 172, "cyvcf2": [172, 173, 174], "bed_read": 172, "novel": 172, "2021": 172, "uk": [172, 174], "zealand": 172, "hesit": 172, "feedback": 172, "mac": 173, "bioconda": 173, "read_x": 173, "x_to_zarr": 173, "speak": 173, "paid": 173, "newli": 173, "consolid": 173, "bgen_to_zarr": 173, "todo": 173, "count_allel": 173, "realist": 173, "my_call_genotyp": 173, "my_call_allele_count": 173, "traceback": 173, "175": 173, "115": 173, "117": 173, "172": 173, "173": 173, "174": 173, "define_variable_if_abs": 173, "176": 173, "177": 173, "178": 173, "179": 173, "279": 173, "default_variable_nam": 173, "variable_nam": 173, "func": 173, "277": 173, "278": 173, "280": 173, "282": 173, "plu": 173, "unchang": 173, "thrown": 173, "catch_warn": 173, "categori": 173, "__name__": [173, 174], "messag": 173, "mergewarn": 173, "my_variant_allele_count": 173, "12kb": 173, "405": 173, "properti": 173, "difficult": 173, "briefli": 173, "critic": 173, "finish": 173, "alt_allele_count": 173, "ndindex": 173, "njit": 173, "ml": 173, "remot": 173, "thread": [173, 174], "kubernet": 173, "jobqueu": 173, "pb": 173, "slurm": 173, "moab": 173, "sge": 173, "lsf": 173, "htcondor": 173, "aw": 173, "gcp": [173, 174], "mpi": 173, "coil": 173, "research": 173, "institut": 173, "job": [173, 174], "schedul": [173, 174], "lf": 173, "connect": 173, "repl": 173, "adjust": 173, "fly": 173, "login": 173, "submiss": 173, "privileg": 173, "dask_jobqueu": 173, "lsfcluster": 173, "16gb": 173, "myproject": 173, "queue": 173, "myqueu": 173, "walltim": 173, "use_stdin": 173, "lsf_unit": 173, "job_script_proloug": 173, "gracefulli": 173, "reach": 173, "wallclock": 173, "shorter": [173, 174], "worker_extra_arg": 173, "lifetim": 173, "350m": 173, "stagger": 173, "5m": 173, "view": 173, "dashboard": [173, 174], "address": 173, "dashboard_link": 173, "launch": 173, "At": 173, "visibl": 173, "adapt": 173, "queu": 173, "prevent": 173, "idl": 173, "short": 173, "wait_count": 173, "120": 173, "thousand": 173, "cycl": 173, "wait": 173, "scheduler_address": 173, "constructor": 173, "8786": 173, "mydata": 173, "diagnost": 173, "progress": [173, 174], "progressbar": 173, "165": 173, "resourceprofil": 173, "profil": 173, "stream": 173, "bottleneck": 173, "optimize_graph": 173, "ipython": 173, "keyword": 173, "cmap": 173, "autumn": 173, "penwidth": 173, "circular": 173, "box": 173, "red": 173, "yellow": 173, "acceler": 173, "recompil": 173, "session": 173, "occasion": 173, "cython": 174, "htslib": 174, "industri": 174, "resid": 174, "amazon": 174, "googl": 174, "read_scikit_allel_vcfzarr": 174, "ceutrio": 174, "gatk3": 174, "19910": 174, "u7": 174, "max_variant_allele_length": 174, "max_variant_id_length": 174, "scene": 174, "chr": 174, "beg": 174, "partition_into_region": 174, "10108928": 174, "10108929": 174, "10207232": 174, "10207233": 174, "10027008": 174, "10027009": 174, "10043392": 174, "10043393": 174, "10141696": 174, "10141697": 174, "10174464": 174, "10174465": 174, "10190848": 174, "10190849": 174, "100_000": 174, "special": 174, "One": 174, "abil": 174, "word": 174, "honor": 174, "wherea": 174, "solut": 174, "slight": 174, "s3f": 174, "gcsf": 174, "credenti": 174, "reli": 174, "offer": 174, "lot": 174, "tri": 174, "benefit": 174, "delta": 174, "numcodec": 174, "codec": 174, "explor": 174, "know": 174, "fixedscaleoffset": 174, "call_d": 174, "f4": 174, "quantiz": 174, "float16": 174, "bitround": 174, "mechan": 174, "debug": 174, "four": 174, "polysom": 174, "polyploidi": 174, "took": 174, "hour": 174, "vcpu": 174, "128gb": 174, "e2": 174, "ftp": 174, "mkdir": 174, "wget": 174, "1000genom": 174, "ebi": 174, "vol1": 174, "20130502": 174, "phase3_shapeit2_mvncall_integrated_v5b": 174, "__main__": 174, "n_worker": 174, "threads_per_work": 174, "multiprocess": 174, "overcommit": 174, "coars": 174, "grain": 174, "minut": 174, "81271745": 174, "2504": 174, "max_alt_alleles_seen": 174}, "objects": {"sgkit": [[7, 0, 1, "", "Fst"], [8, 0, 1, "", "Garud_H"], [9, 0, 1, "", "Tajimas_D"], [10, 0, 1, "", "Weir_Goudet_beta"], [11, 0, 1, "", "call_allele_frequencies"], [12, 0, 1, "", "cohort_allele_frequencies"], [13, 0, 1, "", "convert_call_to_index"], [14, 0, 1, "", "convert_probability_to_call"], [15, 0, 1, "", "count_call_alleles"], [16, 0, 1, "", "count_cohort_alleles"], [17, 0, 1, "", "count_variant_alleles"], [18, 0, 1, "", "count_variant_genotypes"], [19, 0, 1, "", "display_genotypes"], [20, 0, 1, "", "display_pedigree"], [21, 0, 1, "", "divergence"], [22, 0, 1, "", "diversity"], [23, 0, 1, "", "filter_partial_calls"], [24, 0, 1, "", "genee"], [25, 0, 1, "", "genomic_relationship"], [26, 0, 1, "", "gwas_linear_regression"], [27, 0, 1, "", "hardy_weinberg_test"], [28, 0, 1, "", "hybrid_inverse_relationship"], [29, 0, 1, "", "hybrid_relationship"], [30, 0, 1, "", "identity_by_state"], [31, 0, 1, "", "individual_heterozygosity"], [32, 0, 1, "", "infer_call_ploidy"], [33, 0, 1, "", "infer_sample_ploidy"], [34, 0, 1, "", "infer_variant_ploidy"], [35, 0, 1, "", "invert_relationship_matrix"], [51, 0, 1, "", "ld_matrix"], [52, 0, 1, "", "ld_prune"], [53, 0, 1, "", "load_dataset"], [54, 0, 1, "", "maximal_independent_set"], [55, 0, 1, "", "observed_heterozygosity"], [56, 0, 1, "", "pairwise_distance"], [57, 0, 1, "", "parent_indices"], [58, 0, 1, "", "pbs"], [59, 0, 1, "", "pc_relate"], [60, 0, 1, "", "pedigree_contribution"], [61, 0, 1, "", "pedigree_inbreeding"], [62, 0, 1, "", "pedigree_inverse_kinship"], [63, 0, 1, "", "pedigree_kinship"], [64, 0, 1, "", "pedigree_sel"], [65, 0, 1, "", "read_scikit_allel_vcfzarr"], [66, 0, 1, "", "regenie"], [67, 0, 1, "", "sample_stats"], [68, 0, 1, "", "save_dataset"], [69, 0, 1, "", "simulate_genedrop"], [70, 0, 1, "", "simulate_genotype_call_dataset"], [163, 0, 1, "", "variant_stats"], [164, 0, 1, "", "window_by_genome"], [165, 0, 1, "", "window_by_interval"], [166, 0, 1, "", "window_by_position"], [167, 0, 1, "", "window_by_variant"]], "sgkit.io.bgen": [[36, 0, 1, "", "bgen_to_zarr"], [37, 0, 1, "", "read_bgen"], [38, 0, 1, "", "rechunk_bgen"]], "sgkit.io.plink": [[39, 0, 1, "", "plink_to_zarr"], [40, 0, 1, "", "read_plink"], [41, 0, 1, "", "write_plink"], [42, 0, 1, "", "zarr_to_plink"]], "sgkit.io.vcf": [[43, 0, 1, "", "concat_zarrs"], [44, 0, 1, "", "partition_into_regions"], [45, 0, 1, "", "read_vcf"], [46, 0, 1, "", "vcf_to_zarr"], [47, 0, 1, "", "vcf_to_zarrs"], [48, 0, 1, "", "write_vcf"], [49, 0, 1, "", "zarr_array_sizes"], [50, 0, 1, "", "zarr_to_vcf"]], "sgkit.variables": [[71, 1, 1, "", "call_allele_count_spec"], [72, 1, 1, "", "call_allele_frequency_spec"], [73, 1, 1, "", "call_dosage_mask_spec"], [74, 1, 1, "", "call_dosage_spec"], [75, 1, 1, "", "call_genotype_complete_mask_spec"], [76, 1, 1, "", "call_genotype_complete_spec"], [77, 1, 1, "", "call_genotype_fill_spec"], [78, 1, 1, "", "call_genotype_index_mask_spec"], [79, 1, 1, "", "call_genotype_index_spec"], [80, 1, 1, "", "call_genotype_mask_spec"], [81, 1, 1, "", "call_genotype_phased_spec"], [82, 1, 1, "", "call_genotype_probability_mask_spec"], [83, 1, 1, "", "call_genotype_probability_spec"], [84, 1, 1, "", "call_genotype_spec"], [85, 1, 1, "", "call_heterozygosity_spec"], [86, 1, 1, "", "call_ploidy_spec"], [87, 1, 1, "", "cohort_allele_count_spec"], [88, 1, 1, "", "cohort_allele_frequency_spec"], [89, 1, 1, "", "covariates_spec"], [90, 1, 1, "", "interval_contig_name_spec"], [91, 1, 1, "", "interval_start_spec"], [92, 1, 1, "", "interval_stop_spec"], [93, 1, 1, "", "ld_prune_index_to_drop_spec"], [94, 1, 1, "", "parent_id_spec"], [95, 1, 1, "", "parent_spec"], [96, 1, 1, "", "pc_relate_phi_spec"], [97, 1, 1, "", "regenie_base_prediction_spec"], [98, 1, 1, "", "regenie_loco_prediction_spec"], [99, 1, 1, "", "regenie_meta_prediction_spec"], [100, 1, 1, "", "sample_call_rate_spec"], [101, 1, 1, "", "sample_cohort_spec"], [102, 1, 1, "", "sample_id_spec"], [103, 1, 1, "", "sample_n_called_spec"], [104, 1, 1, "", "sample_n_het_spec"], [105, 1, 1, "", "sample_n_hom_alt_spec"], [106, 1, 1, "", "sample_n_hom_ref_spec"], [107, 1, 1, "", "sample_n_non_ref_spec"], [108, 1, 1, "", "sample_pca_component_spec"], [109, 1, 1, "", "sample_pca_explained_variance_ratio_spec"], [110, 1, 1, "", "sample_pca_explained_variance_spec"], [111, 1, 1, "", "sample_pca_loading_spec"], [112, 1, 1, "", "sample_pca_projection_spec"], [113, 1, 1, "", "sample_ploidy_spec"], [114, 1, 1, "", "stat_Fst_spec"], [115, 1, 1, "", "stat_Garud_h123_spec"], [116, 1, 1, "", "stat_Garud_h12_spec"], [117, 1, 1, "", "stat_Garud_h1_spec"], [118, 1, 1, "", "stat_Garud_h2_h1_spec"], [119, 1, 1, "", "stat_Hamilton_Kerr_lambda_spec"], [120, 1, 1, "", "stat_Hamilton_Kerr_tau_spec"], [121, 1, 1, "", "stat_Tajimas_D_spec"], [122, 1, 1, "", "stat_Weir_Goudet_beta_spec"], [123, 1, 1, "", "stat_divergence_spec"], [124, 1, 1, "", "stat_diversity_spec"], [125, 1, 1, "", "stat_genomic_kinship_spec"], [126, 1, 1, "", "stat_genomic_relationship_spec"], [127, 1, 1, "", "stat_hybrid_inverse_relationship_spec"], [128, 1, 1, "", "stat_hybrid_relationship_spec"], [129, 1, 1, "", "stat_identity_by_state_spec"], [130, 1, 1, "", "stat_inverse_relationship_spec"], [131, 1, 1, "", "stat_observed_heterozygosity_spec"], [132, 1, 1, "", "stat_pbs_spec"], [133, 1, 1, "", "stat_pedigree_contribution_spec"], [134, 1, 1, "", "stat_pedigree_inbreeding_spec"], [135, 1, 1, "", "stat_pedigree_inverse_kinship_spec"], [136, 1, 1, "", "stat_pedigree_inverse_relationship_spec"], [137, 1, 1, "", "stat_pedigree_kinship_spec"], [138, 1, 1, "", "stat_pedigree_relationship_spec"], [139, 1, 1, "", "traits_spec"], [140, 1, 1, "", "variant_allele_count_spec"], [141, 1, 1, "", "variant_allele_frequency_spec"], [142, 1, 1, "", "variant_allele_spec"], [143, 1, 1, "", "variant_allele_total_spec"], [144, 1, 1, "", "variant_call_rate_spec"], [145, 1, 1, "", "variant_contig_spec"], [146, 1, 1, "", "variant_genotype_count_spec"], [147, 1, 1, "", "variant_hwe_p_value_spec"], [148, 1, 1, "", "variant_id_spec"], [149, 1, 1, "", "variant_linreg_beta_spec"], [150, 1, 1, "", "variant_linreg_p_value_spec"], [151, 1, 1, "", "variant_linreg_t_value_spec"], [152, 1, 1, "", "variant_n_called_spec"], [153, 1, 1, "", "variant_n_het_spec"], [154, 1, 1, "", "variant_n_hom_alt_spec"], [155, 1, 1, "", "variant_n_hom_ref_spec"], [156, 1, 1, "", "variant_n_non_ref_spec"], [157, 1, 1, "", "variant_ploidy_spec"], [158, 1, 1, "", "variant_position_spec"], [159, 1, 1, "", "variant_score_spec"], [160, 1, 1, "", "window_contig_spec"], [161, 1, 1, "", "window_start_spec"], [162, 1, 1, "", "window_stop_spec"]]}, "objtypes": {"0": "py:function", "1": "py:data"}, "objnames": {"0": ["py", "function", "Python function"], "1": ["py", "data", "Python data"]}, "titleterms": {"about": 0, "api": [1, 3], "refer": [1, 6], "io": [1, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "import": [1, 4], "export": 1, "bgen": [1, 36, 37, 38, 173], "plink": [1, 39, 40, 41, 42, 173], "vcf": [1, 4, 43, 44, 45, 46, 47, 48, 49, 50, 173, 174], "read": [1, 6, 173, 174], "write": [1, 173], "dataset": [1, 3, 6, 169, 173, 174], "method": [1, 168, 169, 173], "basic": 1, "genet": [1, 168, 170, 173], "statist": [1, 170], "popul": 1, "related": [1, 6], "linkag": 1, "disequilibrium": 1, "associ": 1, "regress": 1, "miscellan": 1, "util": 1, "variabl": [1, 3, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 169, 173], "changelog": 2, "0": 2, "10": 2, "unreleas": 2, "new": [2, 169, 171], "featur": 2, "document": [2, 3], "9": 2, "24": 2, "june": 2, "2024": 2, "deprec": 2, "improv": 2, "8": 2, "1": 2, "mai": 2, "bug": 2, "fix": 2, "7": 2, "2": 2, "2023": 2, "break": 2, "chang": 2, "6": 2, "februari": 2, "contribut": 3, "sgkit": [3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 170, 172, 173, 174], "tabl": [3, 168, 170, 173, 174], "content": [3, 168, 170, 173, 174], "discuss": 3, "forum": 3, "code": 3, "repositori": 3, "issu": 3, "develop": 3, "environ": 3, "download": [3, 4, 6, 174], "instal": [3, 168, 173, 174], "run": [3, 174], "test": [3, 169], "continu": 3, "integr": 3, "docstr": 3, "standard": 3, "pr": 3, "git": 3, "op": 3, "python": [3, 170, 173], "depend": 3, "benchmark": 3, "review": 3, "process": 3, "design": 3, "subclass": 3, "type": 3, "delai": 3, "invari": 3, "check": 3, "mix": [3, 174], "ploidi": [3, 174], "numba": [3, 173], "guvector": 3, "usag": [3, 174], "namespac": 3, "gwa": 4, "tutori": [4, 6], "public": 4, "1000": [4, 174], "genom": [4, 6, 169, 174], "data": [4, 6, 168, 173, 174], "from": [4, 169], "get": [4, 168, 169], "know": 4, "our": 4, "ad": [4, 169, 173], "column": 4, "field": 4, "queri": 4, "function": 4, "qualiti": 4, "control": 4, "let": 4, "": 4, "do": [4, 169], "confound": 4, "exampl": [5, 174], "pig": 6, "pedigre": 6, "work": [6, 173], "relationship": 6, "The": 6, "vanraden": 6, "grm": 6, "A": 6, "better": 6, "estim": 6, "ancestr": 6, "allel": 6, "frequenc": 6, "weir": 6, "goudet": 6, "hybrid": 6, "matric": 6, "fst": 7, "garud_h": 8, "tajimas_d": 9, "weir_goudet_beta": 10, "call_allele_frequ": 11, "cohort_allele_frequ": 12, "convert_call_to_index": 13, "convert_probability_to_cal": 14, "count_call_allel": 15, "count_cohort_allel": 16, "count_variant_allel": 17, "count_variant_genotyp": 18, "display_genotyp": 19, "display_pedigre": 20, "diverg": 21, "divers": 22, "filter_partial_cal": 23, "gene": 24, "genomic_relationship": 25, "gwas_linear_regress": 26, "hardy_weinberg_test": 27, "hybrid_inverse_relationship": 28, "hybrid_relationship": 29, "identity_by_st": 30, "individual_heterozygos": 31, "infer_call_ploidi": 32, "infer_sample_ploidi": 33, "infer_variant_ploidi": 34, "invert_relationship_matrix": 35, "bgen_to_zarr": 36, "read_bgen": 37, "rechunk_bgen": 38, "plink_to_zarr": 39, "read_plink": 40, "write_plink": 41, "zarr_to_plink": 42, "concat_zarr": 43, "partition_into_region": 44, "read_vcf": 45, "vcf_to_zarr": [46, 47], "write_vcf": 48, "zarr_array_s": 49, "zarr_to_vcf": 50, "ld_matrix": 51, "ld_prune": 52, "load_dataset": 53, "maximal_independent_set": 54, "observed_heterozygos": 55, "pairwise_dist": 56, "parent_indic": 57, "pb": 58, "pc_relat": 59, "pedigree_contribut": 60, "pedigree_inbreed": 61, "pedigree_inverse_kinship": 62, "pedigree_kinship": 63, "pedigree_sel": 64, "read_scikit_allel_vcfzarr": 65, "regeni": 66, "sample_stat": 67, "save_dataset": 68, "simulate_genedrop": 69, "simulate_genotype_call_dataset": 70, "call_allele_count_spec": 71, "call_allele_frequency_spec": 72, "call_dosage_mask_spec": 73, "call_dosage_spec": 74, "call_genotype_complete_mask_spec": 75, "call_genotype_complete_spec": 76, "call_genotype_fill_spec": 77, "call_genotype_index_mask_spec": 78, "call_genotype_index_spec": 79, "call_genotype_mask_spec": 80, "call_genotype_phased_spec": 81, "call_genotype_probability_mask_spec": 82, "call_genotype_probability_spec": 83, "call_genotype_spec": 84, "call_heterozygosity_spec": 85, "call_ploidy_spec": 86, "cohort_allele_count_spec": 87, "cohort_allele_frequency_spec": 88, "covariates_spec": 89, "interval_contig_name_spec": 90, "interval_start_spec": 91, "interval_stop_spec": 92, "ld_prune_index_to_drop_spec": 93, "parent_id_spec": 94, "parent_spec": 95, "pc_relate_phi_spec": 96, "regenie_base_prediction_spec": 97, "regenie_loco_prediction_spec": 98, "regenie_meta_prediction_spec": 99, "sample_call_rate_spec": 100, "sample_cohort_spec": 101, "sample_id_spec": 102, "sample_n_called_spec": 103, "sample_n_het_spec": 104, "sample_n_hom_alt_spec": 105, "sample_n_hom_ref_spec": 106, "sample_n_non_ref_spec": 107, "sample_pca_component_spec": 108, "sample_pca_explained_variance_ratio_spec": 109, "sample_pca_explained_variance_spec": 110, "sample_pca_loading_spec": 111, "sample_pca_projection_spec": 112, "sample_ploidy_spec": 113, "stat_fst_spec": 114, "stat_garud_h123_spec": 115, "stat_garud_h12_spec": 116, "stat_garud_h1_spec": 117, "stat_garud_h2_h1_spec": 118, "stat_hamilton_kerr_lambda_spec": 119, "stat_hamilton_kerr_tau_spec": 120, "stat_tajimas_d_spec": 121, "stat_weir_goudet_beta_spec": 122, "stat_divergence_spec": 123, "stat_diversity_spec": 124, "stat_genomic_kinship_spec": 125, "stat_genomic_relationship_spec": 126, "stat_hybrid_inverse_relationship_spec": 127, "stat_hybrid_relationship_spec": 128, "stat_identity_by_state_spec": 129, "stat_inverse_relationship_spec": 130, "stat_observed_heterozygosity_spec": 131, "stat_pbs_spec": 132, "stat_pedigree_contribution_spec": 133, "stat_pedigree_inbreeding_spec": 134, "stat_pedigree_inverse_kinship_spec": 135, "stat_pedigree_inverse_relationship_spec": 136, "stat_pedigree_kinship_spec": 137, "stat_pedigree_relationship_spec": 138, "traits_spec": 139, "variant_allele_count_spec": 140, "variant_allele_frequency_spec": 141, "variant_allele_spec": 142, "variant_allele_total_spec": 143, "variant_call_rate_spec": 144, "variant_contig_spec": 145, "variant_genotype_count_spec": 146, "variant_hwe_p_value_spec": 147, "variant_id_spec": 148, "variant_linreg_beta_spec": 149, "variant_linreg_p_value_spec": 150, "variant_linreg_t_value_spec": 151, "variant_n_called_spec": 152, "variant_n_het_spec": 153, "variant_n_hom_alt_spec": 154, "variant_n_hom_ref_spec": 155, "variant_n_non_ref_spec": 156, "variant_ploidy_spec": 157, "variant_position_spec": 158, "variant_score_spec": 159, "window_contig_spec": 160, "window_start_spec": 161, "window_stop_spec": 162, "variant_stat": 163, "window_by_genom": 164, "window_by_interv": 165, "window_by_posit": 166, "window_by_vari": 167, "start": 168, "overview": 168, "structur": 168, "miss": 168, "window": 168, "cohort": 168, "chain": 168, "oper": [168, 173, 174], "chunk": [168, 174], "arrai": 168, "how": 169, "i": 169, "creat": 169, "look": 169, "summari": 169, "valu": 169, "find": 169, "definit": 169, "genotyp": 169, "subset": 169, "rang": 169, "list": 169, "sampl": 169, "defin": 169, "base": 169, "other": [169, 173], "stat": 169, "filter": 169, "variant": 169, "which": 169, "were": 169, "save": 169, "result": 169, "zarr": [169, 173, 174], "file": [169, 174], "load": 169, "toolkit": 170, "indic": 170, "introduc": 172, "user": 173, "guid": 173, "convert": [173, 174], "cloud": [173, 174], "nativ": 173, "merg": 173, "behavior": 173, "interop": 173, "librari": 173, "custom": 173, "name": 173, "convent": 173, "comput": 173, "pca": 173, "deploy": 173, "deploi": 173, "cluster": 173, "us": 173, "gpu": 173, "troubleshoot": 173, "monitor": 173, "visual": 173, "disabl": 173, "cach": 173, "highlight": 174, "multipl": 174, "partit": 174, "size": 174, "storag": 174, "compress": 174, "low": 174, "level": 174, "polyploid": 174, "convers": 174, "inspect": 174}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "scanpydoc.elegant_typehints": 1, "sphinx.ext.intersphinx": 1, "scanpydoc.autosummary_generate_imported": 1, "scanpydoc.definition_list_typed_field": 1, "scanpydoc.rtd_github_links": 1, "scanpydoc": 1, "sphinx": 57}, "alltitles": {"About": [[0, "about"]], "API reference": [[1, "api-reference"]], "IO/imports and exports": [[1, "io-imports-and-exports"]], "BGEN": [[1, "bgen"], [173, "bgen"]], "PLINK": [[1, "plink"], [173, "plink"]], "VCF (reading)": [[1, "vcf-reading"]], "VCF (writing)": [[1, "vcf-writing"]], "Dataset": [[1, "dataset"]], "Methods": [[1, "methods"], [173, "methods"]], "Basic genetics statistics": [[1, "basic-genetics-statistics"]], "Population genetic statistics": [[1, "population-genetic-statistics"]], "Relatedness": [[1, "relatedness"]], "Linkage Disequilibrium": [[1, "linkage-disequilibrium"]], "Genetic Association and Regression": [[1, "genetic-association-and-regression"]], "Miscellaneous": [[1, "miscellaneous"]], "Utilities": [[1, "utilities"]], "Variables": [[1, "variables"]], "Changelog": [[2, "changelog"]], "0.10.0 (unreleased)": [[2, "unreleased"]], "New Features": [[2, "new-features"], [2, "id1"], [2, "id4"], [2, "id8"]], "Documentation": [[2, "documentation"], [2, "id3"]], "0.9.0 (24 June 2024)": [[2, "june-2024"]], "Deprecations": [[2, "deprecations"], [2, "id5"]], "Improvements": [[2, "improvements"], [2, "id2"], [2, "id6"], [2, "id10"]], "0.8.0 (1 May 2024)": [[2, "may-2024"]], "Bug fixes": [[2, "bug-fixes"], [2, "id7"], [2, "id11"]], "0.7.0 (2 May 2023)": [[2, "may-2023"]], "Breaking changes": [[2, "breaking-changes"], [2, "id9"]], "0.6.0 (1 February 2023)": [[2, "february-2023"]], "Contributing to sgkit": [[3, "contributing-to-sgkit"]], "Table of contents:": [[3, "table-of-contents"], [168, "table-of-contents"], [173, "table-of-contents"], [174, "table-of-contents"]], "Discussion forums": [[3, "discussion-forums"]], "Code repositories": [[3, "code-repositories"]], "Issues": [[3, "issues"]], "Development environment": [[3, "development-environment"]], "Download code": [[3, "download-code"]], "Install": [[3, "install"]], "Run tests": [[3, "run-tests"]], "Contributing to code": [[3, "contributing-to-code"]], "Continuous Integration": [[3, "continuous-integration"]], "Test": [[3, "test"]], "Docstrings": [[3, "docstrings"]], "Coding standards": [[3, "coding-standards"]], "PR/Git ops": [[3, "pr-git-ops"]], "Python dependencies": [[3, "python-dependencies"]], "Contributing to documentation": [[3, "contributing-to-documentation"]], "Benchmarks": [[3, "benchmarks"]], "Review process": [[3, "review-process"]], "Design discussions": [[3, "design-discussions"]], "Dataset subclassing": [[3, "dataset-subclassing"]], "Dataset API typing": [[3, "dataset-api-typing"]], "Dataset variables": [[3, "dataset-variables"]], "Delayed invariant checks": [[3, "delayed-invariant-checks"]], "Mixed ploidy": [[3, "mixed-ploidy"]], "Numba guvectorize usage": [[3, "numba-guvectorize-usage"]], "API namespace": [[3, "api-namespace"]], "GWAS Tutorial": [[4, "gwas-tutorial"]], "Download public 1000 Genomes data": [[4, "download-public-1000-genomes-data"]], "Importing data from VCF": [[4, "importing-data-from-vcf"]], "Getting to know our data": [[4, "getting-to-know-our-data"]], "Adding column fields": [[4, "adding-column-fields"]], "Query functions": [[4, "query-functions"]], "Quality control": [[4, "quality-control"]], "Let\u2019s do a GWAS!": [[4, "let-s-do-a-gwas"]], "Confounded!": [[4, "confounded"]], "Examples": [[5, "examples"]], "Relatedness Tutorial": [[6, "relatedness-tutorial"]], "Download the pig dataset": [[6, "download-the-pig-dataset"]], "Reading pedigree data": [[6, "reading-pedigree-data"]], "Working with pedigree data": [[6, "working-with-pedigree-data"]], "Pedigree relationships": [[6, "pedigree-relationships"]], "Genomic relationships": [[6, "genomic-relationships"]], "The VanRaden GRM": [[6, "the-vanraden-grm"]], "A better estimate of ancestral allele frequencies": [[6, "a-better-estimate-of-ancestral-allele-frequencies"]], "Weir-Goudet GRM": [[6, "weir-goudet-grm"]], "Hybrid relationship matrices": [[6, "hybrid-relationship-matrices"]], "References": [[6, "references"]], "sgkit.Fst": [[7, "sgkit-fst"]], "sgkit.Garud_H": [[8, "sgkit-garud-h"]], "sgkit.Tajimas_D": [[9, "sgkit-tajimas-d"]], "sgkit.Weir_Goudet_beta": [[10, "sgkit-weir-goudet-beta"]], "sgkit.call_allele_frequencies": [[11, "sgkit-call-allele-frequencies"]], "sgkit.cohort_allele_frequencies": [[12, "sgkit-cohort-allele-frequencies"]], "sgkit.convert_call_to_index": [[13, "sgkit-convert-call-to-index"]], "sgkit.convert_probability_to_call": [[14, "sgkit-convert-probability-to-call"]], "sgkit.count_call_alleles": [[15, "sgkit-count-call-alleles"]], "sgkit.count_cohort_alleles": [[16, "sgkit-count-cohort-alleles"]], "sgkit.count_variant_alleles": [[17, "sgkit-count-variant-alleles"]], "sgkit.count_variant_genotypes": [[18, "sgkit-count-variant-genotypes"]], "sgkit.display_genotypes": [[19, "sgkit-display-genotypes"]], "sgkit.display_pedigree": [[20, "sgkit-display-pedigree"]], "sgkit.divergence": [[21, "sgkit-divergence"]], "sgkit.diversity": [[22, "sgkit-diversity"]], "sgkit.filter_partial_calls": [[23, "sgkit-filter-partial-calls"]], "sgkit.genee": [[24, "sgkit-genee"]], "sgkit.genomic_relationship": [[25, "sgkit-genomic-relationship"]], "sgkit.gwas_linear_regression": [[26, "sgkit-gwas-linear-regression"]], "sgkit.hardy_weinberg_test": [[27, "sgkit-hardy-weinberg-test"]], "sgkit.hybrid_inverse_relationship": [[28, "sgkit-hybrid-inverse-relationship"]], "sgkit.hybrid_relationship": [[29, "sgkit-hybrid-relationship"]], "sgkit.identity_by_state": [[30, "sgkit-identity-by-state"]], "sgkit.individual_heterozygosity": [[31, "sgkit-individual-heterozygosity"]], "sgkit.infer_call_ploidy": [[32, "sgkit-infer-call-ploidy"]], "sgkit.infer_sample_ploidy": [[33, "sgkit-infer-sample-ploidy"]], "sgkit.infer_variant_ploidy": [[34, "sgkit-infer-variant-ploidy"]], "sgkit.invert_relationship_matrix": [[35, "sgkit-invert-relationship-matrix"]], "sgkit.io.bgen.bgen_to_zarr": [[36, "sgkit-io-bgen-bgen-to-zarr"]], "sgkit.io.bgen.read_bgen": [[37, "sgkit-io-bgen-read-bgen"]], "sgkit.io.bgen.rechunk_bgen": [[38, "sgkit-io-bgen-rechunk-bgen"]], "sgkit.io.plink.plink_to_zarr": [[39, "sgkit-io-plink-plink-to-zarr"]], "sgkit.io.plink.read_plink": [[40, "sgkit-io-plink-read-plink"]], "sgkit.io.plink.write_plink": [[41, "sgkit-io-plink-write-plink"]], "sgkit.io.plink.zarr_to_plink": [[42, "sgkit-io-plink-zarr-to-plink"]], "sgkit.io.vcf.concat_zarrs": [[43, "sgkit-io-vcf-concat-zarrs"]], "sgkit.io.vcf.partition_into_regions": [[44, "sgkit-io-vcf-partition-into-regions"]], "sgkit.io.vcf.read_vcf": [[45, "sgkit-io-vcf-read-vcf"]], "sgkit.io.vcf.vcf_to_zarr": [[46, "sgkit-io-vcf-vcf-to-zarr"]], "sgkit.io.vcf.vcf_to_zarrs": [[47, "sgkit-io-vcf-vcf-to-zarrs"]], "sgkit.io.vcf.write_vcf": [[48, "sgkit-io-vcf-write-vcf"]], "sgkit.io.vcf.zarr_array_sizes": [[49, "sgkit-io-vcf-zarr-array-sizes"]], "sgkit.io.vcf.zarr_to_vcf": [[50, "sgkit-io-vcf-zarr-to-vcf"]], "sgkit.ld_matrix": [[51, "sgkit-ld-matrix"]], "sgkit.ld_prune": [[52, "sgkit-ld-prune"]], "sgkit.load_dataset": [[53, "sgkit-load-dataset"]], "sgkit.maximal_independent_set": [[54, "sgkit-maximal-independent-set"]], "sgkit.observed_heterozygosity": [[55, "sgkit-observed-heterozygosity"]], "sgkit.pairwise_distance": [[56, "sgkit-pairwise-distance"]], "sgkit.parent_indices": [[57, "sgkit-parent-indices"]], "sgkit.pbs": [[58, "sgkit-pbs"]], "sgkit.pc_relate": [[59, "sgkit-pc-relate"]], "sgkit.pedigree_contribution": [[60, "sgkit-pedigree-contribution"]], "sgkit.pedigree_inbreeding": [[61, "sgkit-pedigree-inbreeding"]], "sgkit.pedigree_inverse_kinship": [[62, "sgkit-pedigree-inverse-kinship"]], "sgkit.pedigree_kinship": [[63, "sgkit-pedigree-kinship"]], "sgkit.pedigree_sel": [[64, "sgkit-pedigree-sel"]], "sgkit.read_scikit_allel_vcfzarr": [[65, "sgkit-read-scikit-allel-vcfzarr"]], "sgkit.regenie": [[66, "sgkit-regenie"]], "sgkit.sample_stats": [[67, "sgkit-sample-stats"]], "sgkit.save_dataset": [[68, "sgkit-save-dataset"]], "sgkit.simulate_genedrop": [[69, "sgkit-simulate-genedrop"]], "sgkit.simulate_genotype_call_dataset": [[70, "sgkit-simulate-genotype-call-dataset"]], "sgkit.variables.call_allele_count_spec": [[71, "sgkit-variables-call-allele-count-spec"]], "sgkit.variables.call_allele_frequency_spec": [[72, "sgkit-variables-call-allele-frequency-spec"]], "sgkit.variables.call_dosage_mask_spec": [[73, "sgkit-variables-call-dosage-mask-spec"]], "sgkit.variables.call_dosage_spec": [[74, "sgkit-variables-call-dosage-spec"]], "sgkit.variables.call_genotype_complete_mask_spec": [[75, "sgkit-variables-call-genotype-complete-mask-spec"]], "sgkit.variables.call_genotype_complete_spec": [[76, "sgkit-variables-call-genotype-complete-spec"]], "sgkit.variables.call_genotype_fill_spec": [[77, "sgkit-variables-call-genotype-fill-spec"]], "sgkit.variables.call_genotype_index_mask_spec": [[78, "sgkit-variables-call-genotype-index-mask-spec"]], "sgkit.variables.call_genotype_index_spec": [[79, "sgkit-variables-call-genotype-index-spec"]], "sgkit.variables.call_genotype_mask_spec": [[80, "sgkit-variables-call-genotype-mask-spec"]], "sgkit.variables.call_genotype_phased_spec": [[81, "sgkit-variables-call-genotype-phased-spec"]], "sgkit.variables.call_genotype_probability_mask_spec": [[82, "sgkit-variables-call-genotype-probability-mask-spec"]], "sgkit.variables.call_genotype_probability_spec": [[83, "sgkit-variables-call-genotype-probability-spec"]], "sgkit.variables.call_genotype_spec": [[84, "sgkit-variables-call-genotype-spec"]], "sgkit.variables.call_heterozygosity_spec": [[85, "sgkit-variables-call-heterozygosity-spec"]], "sgkit.variables.call_ploidy_spec": [[86, "sgkit-variables-call-ploidy-spec"]], "sgkit.variables.cohort_allele_count_spec": [[87, "sgkit-variables-cohort-allele-count-spec"]], "sgkit.variables.cohort_allele_frequency_spec": [[88, "sgkit-variables-cohort-allele-frequency-spec"]], "sgkit.variables.covariates_spec": [[89, "sgkit-variables-covariates-spec"]], "sgkit.variables.interval_contig_name_spec": [[90, "sgkit-variables-interval-contig-name-spec"]], "sgkit.variables.interval_start_spec": [[91, "sgkit-variables-interval-start-spec"]], "sgkit.variables.interval_stop_spec": [[92, "sgkit-variables-interval-stop-spec"]], "sgkit.variables.ld_prune_index_to_drop_spec": [[93, "sgkit-variables-ld-prune-index-to-drop-spec"]], "sgkit.variables.parent_id_spec": [[94, "sgkit-variables-parent-id-spec"]], "sgkit.variables.parent_spec": [[95, "sgkit-variables-parent-spec"]], "sgkit.variables.pc_relate_phi_spec": [[96, "sgkit-variables-pc-relate-phi-spec"]], "sgkit.variables.regenie_base_prediction_spec": [[97, "sgkit-variables-regenie-base-prediction-spec"]], "sgkit.variables.regenie_loco_prediction_spec": [[98, "sgkit-variables-regenie-loco-prediction-spec"]], "sgkit.variables.regenie_meta_prediction_spec": [[99, "sgkit-variables-regenie-meta-prediction-spec"]], "sgkit.variables.sample_call_rate_spec": [[100, "sgkit-variables-sample-call-rate-spec"]], "sgkit.variables.sample_cohort_spec": [[101, "sgkit-variables-sample-cohort-spec"]], "sgkit.variables.sample_id_spec": [[102, "sgkit-variables-sample-id-spec"]], "sgkit.variables.sample_n_called_spec": [[103, "sgkit-variables-sample-n-called-spec"]], "sgkit.variables.sample_n_het_spec": [[104, "sgkit-variables-sample-n-het-spec"]], "sgkit.variables.sample_n_hom_alt_spec": [[105, "sgkit-variables-sample-n-hom-alt-spec"]], "sgkit.variables.sample_n_hom_ref_spec": [[106, "sgkit-variables-sample-n-hom-ref-spec"]], "sgkit.variables.sample_n_non_ref_spec": [[107, "sgkit-variables-sample-n-non-ref-spec"]], "sgkit.variables.sample_pca_component_spec": [[108, "sgkit-variables-sample-pca-component-spec"]], "sgkit.variables.sample_pca_explained_variance_ratio_spec": [[109, "sgkit-variables-sample-pca-explained-variance-ratio-spec"]], "sgkit.variables.sample_pca_explained_variance_spec": [[110, "sgkit-variables-sample-pca-explained-variance-spec"]], "sgkit.variables.sample_pca_loading_spec": [[111, "sgkit-variables-sample-pca-loading-spec"]], "sgkit.variables.sample_pca_projection_spec": [[112, "sgkit-variables-sample-pca-projection-spec"]], "sgkit.variables.sample_ploidy_spec": [[113, "sgkit-variables-sample-ploidy-spec"]], "sgkit.variables.stat_Fst_spec": [[114, "sgkit-variables-stat-fst-spec"]], "sgkit.variables.stat_Garud_h123_spec": [[115, "sgkit-variables-stat-garud-h123-spec"]], "sgkit.variables.stat_Garud_h12_spec": [[116, "sgkit-variables-stat-garud-h12-spec"]], "sgkit.variables.stat_Garud_h1_spec": [[117, "sgkit-variables-stat-garud-h1-spec"]], "sgkit.variables.stat_Garud_h2_h1_spec": [[118, "sgkit-variables-stat-garud-h2-h1-spec"]], "sgkit.variables.stat_Hamilton_Kerr_lambda_spec": [[119, "sgkit-variables-stat-hamilton-kerr-lambda-spec"]], "sgkit.variables.stat_Hamilton_Kerr_tau_spec": [[120, "sgkit-variables-stat-hamilton-kerr-tau-spec"]], "sgkit.variables.stat_Tajimas_D_spec": [[121, "sgkit-variables-stat-tajimas-d-spec"]], "sgkit.variables.stat_Weir_Goudet_beta_spec": [[122, "sgkit-variables-stat-weir-goudet-beta-spec"]], "sgkit.variables.stat_divergence_spec": [[123, "sgkit-variables-stat-divergence-spec"]], "sgkit.variables.stat_diversity_spec": [[124, "sgkit-variables-stat-diversity-spec"]], "sgkit.variables.stat_genomic_kinship_spec": [[125, "sgkit-variables-stat-genomic-kinship-spec"]], "sgkit.variables.stat_genomic_relationship_spec": [[126, "sgkit-variables-stat-genomic-relationship-spec"]], "sgkit.variables.stat_hybrid_inverse_relationship_spec": [[127, "sgkit-variables-stat-hybrid-inverse-relationship-spec"]], "sgkit.variables.stat_hybrid_relationship_spec": [[128, "sgkit-variables-stat-hybrid-relationship-spec"]], "sgkit.variables.stat_identity_by_state_spec": [[129, "sgkit-variables-stat-identity-by-state-spec"]], "sgkit.variables.stat_inverse_relationship_spec": [[130, "sgkit-variables-stat-inverse-relationship-spec"]], "sgkit.variables.stat_observed_heterozygosity_spec": [[131, "sgkit-variables-stat-observed-heterozygosity-spec"]], "sgkit.variables.stat_pbs_spec": [[132, "sgkit-variables-stat-pbs-spec"]], "sgkit.variables.stat_pedigree_contribution_spec": [[133, "sgkit-variables-stat-pedigree-contribution-spec"]], "sgkit.variables.stat_pedigree_inbreeding_spec": [[134, "sgkit-variables-stat-pedigree-inbreeding-spec"]], "sgkit.variables.stat_pedigree_inverse_kinship_spec": [[135, "sgkit-variables-stat-pedigree-inverse-kinship-spec"]], "sgkit.variables.stat_pedigree_inverse_relationship_spec": [[136, "sgkit-variables-stat-pedigree-inverse-relationship-spec"]], "sgkit.variables.stat_pedigree_kinship_spec": [[137, "sgkit-variables-stat-pedigree-kinship-spec"]], "sgkit.variables.stat_pedigree_relationship_spec": [[138, "sgkit-variables-stat-pedigree-relationship-spec"]], "sgkit.variables.traits_spec": [[139, "sgkit-variables-traits-spec"]], "sgkit.variables.variant_allele_count_spec": [[140, "sgkit-variables-variant-allele-count-spec"]], "sgkit.variables.variant_allele_frequency_spec": [[141, "sgkit-variables-variant-allele-frequency-spec"]], "sgkit.variables.variant_allele_spec": [[142, "sgkit-variables-variant-allele-spec"]], "sgkit.variables.variant_allele_total_spec": [[143, "sgkit-variables-variant-allele-total-spec"]], "sgkit.variables.variant_call_rate_spec": [[144, "sgkit-variables-variant-call-rate-spec"]], "sgkit.variables.variant_contig_spec": [[145, "sgkit-variables-variant-contig-spec"]], "sgkit.variables.variant_genotype_count_spec": [[146, "sgkit-variables-variant-genotype-count-spec"]], "sgkit.variables.variant_hwe_p_value_spec": [[147, "sgkit-variables-variant-hwe-p-value-spec"]], "sgkit.variables.variant_id_spec": [[148, "sgkit-variables-variant-id-spec"]], "sgkit.variables.variant_linreg_beta_spec": [[149, "sgkit-variables-variant-linreg-beta-spec"]], "sgkit.variables.variant_linreg_p_value_spec": [[150, "sgkit-variables-variant-linreg-p-value-spec"]], "sgkit.variables.variant_linreg_t_value_spec": [[151, "sgkit-variables-variant-linreg-t-value-spec"]], "sgkit.variables.variant_n_called_spec": [[152, "sgkit-variables-variant-n-called-spec"]], "sgkit.variables.variant_n_het_spec": [[153, "sgkit-variables-variant-n-het-spec"]], "sgkit.variables.variant_n_hom_alt_spec": [[154, "sgkit-variables-variant-n-hom-alt-spec"]], "sgkit.variables.variant_n_hom_ref_spec": [[155, "sgkit-variables-variant-n-hom-ref-spec"]], "sgkit.variables.variant_n_non_ref_spec": [[156, "sgkit-variables-variant-n-non-ref-spec"]], "sgkit.variables.variant_ploidy_spec": [[157, "sgkit-variables-variant-ploidy-spec"]], "sgkit.variables.variant_position_spec": [[158, "sgkit-variables-variant-position-spec"]], "sgkit.variables.variant_score_spec": [[159, "sgkit-variables-variant-score-spec"]], "sgkit.variables.window_contig_spec": [[160, "sgkit-variables-window-contig-spec"]], "sgkit.variables.window_start_spec": [[161, "sgkit-variables-window-start-spec"]], "sgkit.variables.window_stop_spec": [[162, "sgkit-variables-window-stop-spec"]], "sgkit.variant_stats": [[163, "sgkit-variant-stats"]], "sgkit.window_by_genome": [[164, "sgkit-window-by-genome"]], "sgkit.window_by_interval": [[165, "sgkit-window-by-interval"]], "sgkit.window_by_position": [[166, "sgkit-window-by-position"]], "sgkit.window_by_variant": [[167, "sgkit-window-by-variant"]], "Getting Started": [[168, "getting-started"]], "Installation": [[168, "installation"], [173, "installation"], [174, "installation"]], "Overview": [[168, "overview"]], "Data structures": [[168, "data-structures"]], "Genetic methods": [[168, "genetic-methods"]], "Missing data": [[168, "missing-data"]], "Windowing": [[168, "windowing"]], "Cohorts": [[168, "cohorts"]], "Chaining operations": [[168, "chaining-operations"]], "Chunked arrays": [[168, "chunked-arrays"]], "How do I \u2026": [[169, "how-do-i"]], "Create a test dataset?": [[169, "create-a-test-dataset"]], "Look at the dataset summary?": [[169, "look-at-the-dataset-summary"]], "Get the values for a variable in a dataset?": [[169, "get-the-values-for-a-variable-in-a-dataset"]], "Find the definition for a variable in a dataset?": [[169, "find-the-definition-for-a-variable-in-a-dataset"]], "Look at the genotypes?": [[169, "look-at-the-genotypes"]], "Subset the variables?": [[169, "subset-the-variables"]], "Subset to a genomic range?": [[169, "subset-to-a-genomic-range"]], "Get the list of samples?": [[169, "get-the-list-of-samples"]], "Subset the samples?": [[169, "subset-the-samples"]], "Define a new variable based on others?": [[169, "define-a-new-variable-based-on-others"]], "Get summary stats?": [[169, "get-summary-stats"]], "Filter variants?": [[169, "filter-variants"]], "Find which new variables were added by a method?": [[169, "find-which-new-variables-were-added-by-a-method"]], "Save results to a Zarr file?": [[169, "save-results-to-a-zarr-file"]], "Load a dataset from Zarr?": [[169, "load-a-dataset-from-zarr"]], "sgkit: Statistical genetics toolkit in Python": [[170, "sgkit-statistical-genetics-toolkit-in-python"]], "Contents": [[170, null]], "Indices and tables": [[170, "indices-and-tables"]], "News": [[171, "news"]], "Introducing sgkit": [[172, "introducing-sgkit"]], "User Guide": [[173, "user-guide"]], "Reading and writing genetic data": [[173, "reading-and-writing-genetic-data"]], "Converting genetic data to Zarr": [[173, "converting-genetic-data-to-zarr"]], "VCF": [[173, "vcf"]], "Working with cloud-native data": [[173, "working-with-cloud-native-data"]], "Datasets": [[173, "datasets"]], "Genetic variables": [[173, "genetic-variables"]], "Dataset merge behavior": [[173, "dataset-merge-behavior"]], "Interop with other Python libraries": [[173, "interop-with-other-python-libraries"]], "Custom naming conventions": [[173, "custom-naming-conventions"]], "Adding custom data to a Dataset": [[173, "adding-custom-data-to-a-dataset"]], "Custom Computations": [[173, "custom-computations"]], "PCA": [[173, "pca"]], "Deployment": [[173, "deployment"]], "Deploying sgkit on a cluster": [[173, "deploying-sgkit-on-a-cluster"]], "Using GPUs": [[173, "using-gpus"]], "Troubleshooting": [[173, "troubleshooting"]], "Monitoring operations": [[173, "monitoring-operations"]], "Visualizing computations": [[173, "visualizing-computations"]], "Disabling the Numba cache": [[173, "disabling-the-numba-cache"]], "Reading VCF": [[174, "reading-vcf"]], "Highlights": [[174, "highlights"]], "Usage": [[174, "usage"]], "Multiple files": [[174, "multiple-files"]], "Partitioning": [[174, "partitioning"]], "Chunk sizes": [[174, "chunk-sizes"]], "Cloud storage": [[174, "cloud-storage"]], "Compression": [[174, "compression"]], "Low-level operation": [[174, "low-level-operation"]], "Polyploid and mixed-ploidy VCF": [[174, "polyploid-and-mixed-ploidy-vcf"]], "Example: converting 1000 genomes VCF to Zarr": [[174, "example-converting-1000-genomes-vcf-to-zarr"]], "Install sgkit": [[174, "install-sgkit"]], "Download the data": [[174, "download-the-data"]], "Run the conversion": [[174, "run-the-conversion"]], "Inspect the dataset": [[174, "inspect-the-dataset"]]}, "indexentries": {"fst() (in module sgkit)": [[7, "sgkit.Fst"]], "garud_h() (in module sgkit)": [[8, "sgkit.Garud_H"]], "tajimas_d() (in module sgkit)": [[9, "sgkit.Tajimas_D"]], "weir_goudet_beta() (in module sgkit)": [[10, "sgkit.Weir_Goudet_beta"]], "call_allele_frequencies() (in module sgkit)": [[11, "sgkit.call_allele_frequencies"]], "cohort_allele_frequencies() (in module sgkit)": [[12, "sgkit.cohort_allele_frequencies"]], "convert_call_to_index() (in module sgkit)": [[13, "sgkit.convert_call_to_index"]], "convert_probability_to_call() (in module sgkit)": [[14, "sgkit.convert_probability_to_call"]], "count_call_alleles() (in module sgkit)": [[15, "sgkit.count_call_alleles"]], "count_cohort_alleles() (in module sgkit)": [[16, "sgkit.count_cohort_alleles"]], "count_variant_alleles() (in module sgkit)": [[17, "sgkit.count_variant_alleles"]], "count_variant_genotypes() (in module sgkit)": [[18, "sgkit.count_variant_genotypes"]], "display_genotypes() (in module sgkit)": [[19, "sgkit.display_genotypes"]], "display_pedigree() (in module sgkit)": [[20, "sgkit.display_pedigree"]], "divergence() (in module sgkit)": [[21, "sgkit.divergence"]], "diversity() (in module sgkit)": [[22, "sgkit.diversity"]], "filter_partial_calls() (in module sgkit)": [[23, "sgkit.filter_partial_calls"]], "genee() (in module sgkit)": [[24, "sgkit.genee"]], "genomic_relationship() (in module sgkit)": [[25, "sgkit.genomic_relationship"]], "gwas_linear_regression() (in module sgkit)": [[26, "sgkit.gwas_linear_regression"]], "hardy_weinberg_test() (in module sgkit)": [[27, "sgkit.hardy_weinberg_test"]], "hybrid_inverse_relationship() (in module sgkit)": [[28, "sgkit.hybrid_inverse_relationship"]], "hybrid_relationship() (in module sgkit)": [[29, "sgkit.hybrid_relationship"]], "identity_by_state() (in module sgkit)": [[30, "sgkit.identity_by_state"]], "individual_heterozygosity() (in module sgkit)": [[31, "sgkit.individual_heterozygosity"]], "infer_call_ploidy() (in module sgkit)": [[32, "sgkit.infer_call_ploidy"]], "infer_sample_ploidy() (in module sgkit)": [[33, "sgkit.infer_sample_ploidy"]], "infer_variant_ploidy() (in module sgkit)": [[34, "sgkit.infer_variant_ploidy"]], "invert_relationship_matrix() (in module sgkit)": [[35, "sgkit.invert_relationship_matrix"]], "bgen_to_zarr() (in module sgkit.io.bgen)": [[36, "sgkit.io.bgen.bgen_to_zarr"]], "read_bgen() (in module sgkit.io.bgen)": [[37, "sgkit.io.bgen.read_bgen"]], "rechunk_bgen() (in module sgkit.io.bgen)": [[38, "sgkit.io.bgen.rechunk_bgen"]], "plink_to_zarr() (in module sgkit.io.plink)": [[39, "sgkit.io.plink.plink_to_zarr"]], "read_plink() (in module sgkit.io.plink)": [[40, "sgkit.io.plink.read_plink"]], "write_plink() (in module sgkit.io.plink)": [[41, "sgkit.io.plink.write_plink"]], "zarr_to_plink() (in module sgkit.io.plink)": [[42, "sgkit.io.plink.zarr_to_plink"]], "concat_zarrs() (in module sgkit.io.vcf)": [[43, "sgkit.io.vcf.concat_zarrs"]], "partition_into_regions() (in module sgkit.io.vcf)": [[44, "sgkit.io.vcf.partition_into_regions"]], "read_vcf() (in module sgkit.io.vcf)": [[45, "sgkit.io.vcf.read_vcf"]], "vcf_to_zarr() (in module sgkit.io.vcf)": [[46, "sgkit.io.vcf.vcf_to_zarr"]], "vcf_to_zarrs() (in module sgkit.io.vcf)": [[47, "sgkit.io.vcf.vcf_to_zarrs"]], "write_vcf() (in module sgkit.io.vcf)": [[48, "sgkit.io.vcf.write_vcf"]], "zarr_array_sizes() (in module sgkit.io.vcf)": [[49, "sgkit.io.vcf.zarr_array_sizes"]], "zarr_to_vcf() (in module sgkit.io.vcf)": [[50, "sgkit.io.vcf.zarr_to_vcf"]], "ld_matrix() (in module sgkit)": [[51, "sgkit.ld_matrix"]], "ld_prune() (in module sgkit)": [[52, "sgkit.ld_prune"]], "load_dataset() (in module sgkit)": [[53, "sgkit.load_dataset"]], "maximal_independent_set() (in module sgkit)": [[54, "sgkit.maximal_independent_set"]], "observed_heterozygosity() (in module sgkit)": [[55, "sgkit.observed_heterozygosity"]], "pairwise_distance() (in module sgkit)": [[56, "sgkit.pairwise_distance"]], "parent_indices() (in module sgkit)": [[57, "sgkit.parent_indices"]], "pbs() (in module sgkit)": [[58, "sgkit.pbs"]], "pc_relate() (in module sgkit)": [[59, "sgkit.pc_relate"]], "pedigree_contribution() (in module sgkit)": [[60, "sgkit.pedigree_contribution"]], "pedigree_inbreeding() (in module sgkit)": [[61, "sgkit.pedigree_inbreeding"]], "pedigree_inverse_kinship() (in module sgkit)": [[62, "sgkit.pedigree_inverse_kinship"]], "pedigree_kinship() (in module sgkit)": [[63, "sgkit.pedigree_kinship"]], "pedigree_sel() (in module sgkit)": [[64, "sgkit.pedigree_sel"]], "read_scikit_allel_vcfzarr() (in module sgkit)": [[65, "sgkit.read_scikit_allel_vcfzarr"]], "regenie() (in module sgkit)": [[66, "sgkit.regenie"]], "sample_stats() (in module sgkit)": [[67, "sgkit.sample_stats"]], "save_dataset() (in module sgkit)": [[68, "sgkit.save_dataset"]], "simulate_genedrop() (in module sgkit)": [[69, "sgkit.simulate_genedrop"]], "simulate_genotype_call_dataset() (in module sgkit)": [[70, "sgkit.simulate_genotype_call_dataset"]], "call_allele_count_spec (in module sgkit.variables)": [[71, "sgkit.variables.call_allele_count_spec"]], "call_allele_frequency_spec (in module sgkit.variables)": [[72, "sgkit.variables.call_allele_frequency_spec"]], "call_dosage_mask_spec (in module sgkit.variables)": [[73, "sgkit.variables.call_dosage_mask_spec"]], "call_dosage_spec (in module sgkit.variables)": [[74, "sgkit.variables.call_dosage_spec"]], "call_genotype_complete_mask_spec (in module sgkit.variables)": [[75, "sgkit.variables.call_genotype_complete_mask_spec"]], "call_genotype_complete_spec (in module sgkit.variables)": [[76, "sgkit.variables.call_genotype_complete_spec"]], "call_genotype_fill_spec (in module sgkit.variables)": [[77, "sgkit.variables.call_genotype_fill_spec"]], "call_genotype_index_mask_spec (in module sgkit.variables)": [[78, "sgkit.variables.call_genotype_index_mask_spec"]], "call_genotype_index_spec (in module sgkit.variables)": [[79, "sgkit.variables.call_genotype_index_spec"]], "call_genotype_mask_spec (in module sgkit.variables)": [[80, "sgkit.variables.call_genotype_mask_spec"]], "call_genotype_phased_spec (in module sgkit.variables)": [[81, "sgkit.variables.call_genotype_phased_spec"]], "call_genotype_probability_mask_spec (in module sgkit.variables)": [[82, "sgkit.variables.call_genotype_probability_mask_spec"]], "call_genotype_probability_spec (in module sgkit.variables)": [[83, "sgkit.variables.call_genotype_probability_spec"]], "call_genotype_spec (in module sgkit.variables)": [[84, "sgkit.variables.call_genotype_spec"]], "call_heterozygosity_spec (in module sgkit.variables)": [[85, "sgkit.variables.call_heterozygosity_spec"]], "call_ploidy_spec (in module sgkit.variables)": [[86, "sgkit.variables.call_ploidy_spec"]], "cohort_allele_count_spec (in module sgkit.variables)": [[87, "sgkit.variables.cohort_allele_count_spec"]], "cohort_allele_frequency_spec (in module sgkit.variables)": [[88, "sgkit.variables.cohort_allele_frequency_spec"]], "covariates_spec (in module sgkit.variables)": [[89, "sgkit.variables.covariates_spec"]], "interval_contig_name_spec (in module sgkit.variables)": [[90, "sgkit.variables.interval_contig_name_spec"]], "interval_start_spec (in module sgkit.variables)": [[91, "sgkit.variables.interval_start_spec"]], "interval_stop_spec (in module sgkit.variables)": [[92, "sgkit.variables.interval_stop_spec"]], "ld_prune_index_to_drop_spec (in module sgkit.variables)": [[93, "sgkit.variables.ld_prune_index_to_drop_spec"]], "parent_id_spec (in module sgkit.variables)": [[94, "sgkit.variables.parent_id_spec"]], "parent_spec (in module sgkit.variables)": [[95, "sgkit.variables.parent_spec"]], "pc_relate_phi_spec (in module sgkit.variables)": [[96, "sgkit.variables.pc_relate_phi_spec"]], "regenie_base_prediction_spec (in module sgkit.variables)": [[97, "sgkit.variables.regenie_base_prediction_spec"]], "regenie_loco_prediction_spec (in module sgkit.variables)": [[98, "sgkit.variables.regenie_loco_prediction_spec"]], "regenie_meta_prediction_spec (in module sgkit.variables)": [[99, "sgkit.variables.regenie_meta_prediction_spec"]], "sample_call_rate_spec (in module sgkit.variables)": [[100, "sgkit.variables.sample_call_rate_spec"]], "sample_cohort_spec (in module sgkit.variables)": [[101, "sgkit.variables.sample_cohort_spec"]], "sample_id_spec (in module sgkit.variables)": [[102, "sgkit.variables.sample_id_spec"]], "sample_n_called_spec (in module sgkit.variables)": [[103, "sgkit.variables.sample_n_called_spec"]], "sample_n_het_spec (in module sgkit.variables)": [[104, "sgkit.variables.sample_n_het_spec"]], "sample_n_hom_alt_spec (in module sgkit.variables)": [[105, "sgkit.variables.sample_n_hom_alt_spec"]], "sample_n_hom_ref_spec (in module sgkit.variables)": [[106, "sgkit.variables.sample_n_hom_ref_spec"]], "sample_n_non_ref_spec (in module sgkit.variables)": [[107, "sgkit.variables.sample_n_non_ref_spec"]], "sample_pca_component_spec (in module sgkit.variables)": [[108, "sgkit.variables.sample_pca_component_spec"]], "sample_pca_explained_variance_ratio_spec (in module sgkit.variables)": [[109, "sgkit.variables.sample_pca_explained_variance_ratio_spec"]], "sample_pca_explained_variance_spec (in module sgkit.variables)": [[110, "sgkit.variables.sample_pca_explained_variance_spec"]], "sample_pca_loading_spec (in module sgkit.variables)": [[111, "sgkit.variables.sample_pca_loading_spec"]], "sample_pca_projection_spec (in module sgkit.variables)": [[112, "sgkit.variables.sample_pca_projection_spec"]], "sample_ploidy_spec (in module sgkit.variables)": [[113, "sgkit.variables.sample_ploidy_spec"]], "stat_fst_spec (in module sgkit.variables)": [[114, "sgkit.variables.stat_Fst_spec"]], "stat_garud_h123_spec (in module sgkit.variables)": [[115, "sgkit.variables.stat_Garud_h123_spec"]], "stat_garud_h12_spec (in module sgkit.variables)": [[116, "sgkit.variables.stat_Garud_h12_spec"]], "stat_garud_h1_spec (in module sgkit.variables)": [[117, "sgkit.variables.stat_Garud_h1_spec"]], "stat_garud_h2_h1_spec (in module sgkit.variables)": [[118, "sgkit.variables.stat_Garud_h2_h1_spec"]], "stat_hamilton_kerr_lambda_spec (in module sgkit.variables)": [[119, "sgkit.variables.stat_Hamilton_Kerr_lambda_spec"]], "stat_hamilton_kerr_tau_spec (in module sgkit.variables)": [[120, "sgkit.variables.stat_Hamilton_Kerr_tau_spec"]], "stat_tajimas_d_spec (in module sgkit.variables)": [[121, "sgkit.variables.stat_Tajimas_D_spec"]], "stat_weir_goudet_beta_spec (in module sgkit.variables)": [[122, "sgkit.variables.stat_Weir_Goudet_beta_spec"]], "stat_divergence_spec (in module sgkit.variables)": [[123, "sgkit.variables.stat_divergence_spec"]], "stat_diversity_spec (in module sgkit.variables)": [[124, "sgkit.variables.stat_diversity_spec"]], "stat_genomic_kinship_spec (in module sgkit.variables)": [[125, "sgkit.variables.stat_genomic_kinship_spec"]], "stat_genomic_relationship_spec (in module sgkit.variables)": [[126, "sgkit.variables.stat_genomic_relationship_spec"]], "stat_hybrid_inverse_relationship_spec (in module sgkit.variables)": [[127, "sgkit.variables.stat_hybrid_inverse_relationship_spec"]], "stat_hybrid_relationship_spec (in module sgkit.variables)": [[128, "sgkit.variables.stat_hybrid_relationship_spec"]], "stat_identity_by_state_spec (in module sgkit.variables)": [[129, "sgkit.variables.stat_identity_by_state_spec"]], "stat_inverse_relationship_spec (in module sgkit.variables)": [[130, "sgkit.variables.stat_inverse_relationship_spec"]], "stat_observed_heterozygosity_spec (in module sgkit.variables)": [[131, "sgkit.variables.stat_observed_heterozygosity_spec"]], "stat_pbs_spec (in module sgkit.variables)": [[132, "sgkit.variables.stat_pbs_spec"]], "stat_pedigree_contribution_spec (in module sgkit.variables)": [[133, "sgkit.variables.stat_pedigree_contribution_spec"]], "stat_pedigree_inbreeding_spec (in module sgkit.variables)": [[134, "sgkit.variables.stat_pedigree_inbreeding_spec"]], "stat_pedigree_inverse_kinship_spec (in module sgkit.variables)": [[135, "sgkit.variables.stat_pedigree_inverse_kinship_spec"]], "stat_pedigree_inverse_relationship_spec (in module sgkit.variables)": [[136, "sgkit.variables.stat_pedigree_inverse_relationship_spec"]], "stat_pedigree_kinship_spec (in module sgkit.variables)": [[137, "sgkit.variables.stat_pedigree_kinship_spec"]], "stat_pedigree_relationship_spec (in module sgkit.variables)": [[138, "sgkit.variables.stat_pedigree_relationship_spec"]], "traits_spec (in module sgkit.variables)": [[139, "sgkit.variables.traits_spec"]], "variant_allele_count_spec (in module sgkit.variables)": [[140, "sgkit.variables.variant_allele_count_spec"]], "variant_allele_frequency_spec (in module sgkit.variables)": [[141, "sgkit.variables.variant_allele_frequency_spec"]], "variant_allele_spec (in module sgkit.variables)": [[142, "sgkit.variables.variant_allele_spec"]], "variant_allele_total_spec (in module sgkit.variables)": [[143, "sgkit.variables.variant_allele_total_spec"]], "variant_call_rate_spec (in module sgkit.variables)": [[144, "sgkit.variables.variant_call_rate_spec"]], "variant_contig_spec (in module sgkit.variables)": [[145, "sgkit.variables.variant_contig_spec"]], "variant_genotype_count_spec (in module sgkit.variables)": [[146, "sgkit.variables.variant_genotype_count_spec"]], "variant_hwe_p_value_spec (in module sgkit.variables)": [[147, "sgkit.variables.variant_hwe_p_value_spec"]], "variant_id_spec (in module sgkit.variables)": [[148, "sgkit.variables.variant_id_spec"]], "variant_linreg_beta_spec (in module sgkit.variables)": [[149, "sgkit.variables.variant_linreg_beta_spec"]], "variant_linreg_p_value_spec (in module sgkit.variables)": [[150, "sgkit.variables.variant_linreg_p_value_spec"]], "variant_linreg_t_value_spec (in module sgkit.variables)": [[151, "sgkit.variables.variant_linreg_t_value_spec"]], "variant_n_called_spec (in module sgkit.variables)": [[152, "sgkit.variables.variant_n_called_spec"]], "variant_n_het_spec (in module sgkit.variables)": [[153, "sgkit.variables.variant_n_het_spec"]], "variant_n_hom_alt_spec (in module sgkit.variables)": [[154, "sgkit.variables.variant_n_hom_alt_spec"]], "variant_n_hom_ref_spec (in module sgkit.variables)": [[155, "sgkit.variables.variant_n_hom_ref_spec"]], "variant_n_non_ref_spec (in module sgkit.variables)": [[156, "sgkit.variables.variant_n_non_ref_spec"]], "variant_ploidy_spec (in module sgkit.variables)": [[157, "sgkit.variables.variant_ploidy_spec"]], "variant_position_spec (in module sgkit.variables)": [[158, "sgkit.variables.variant_position_spec"]], "variant_score_spec (in module sgkit.variables)": [[159, "sgkit.variables.variant_score_spec"]], "window_contig_spec (in module sgkit.variables)": [[160, "sgkit.variables.window_contig_spec"]], "window_start_spec (in module sgkit.variables)": [[161, "sgkit.variables.window_start_spec"]], "window_stop_spec (in module sgkit.variables)": [[162, "sgkit.variables.window_stop_spec"]], "variant_stats() (in module sgkit)": [[163, "sgkit.variant_stats"]], "window_by_genome() (in module sgkit)": [[164, "sgkit.window_by_genome"]], "window_by_interval() (in module sgkit)": [[165, "sgkit.window_by_interval"]], "window_by_position() (in module sgkit)": [[166, "sgkit.window_by_position"]], "window_by_variant() (in module sgkit)": [[167, "sgkit.window_by_variant"]]}})
\ No newline at end of file
diff --git a/latest/user_guide.html b/latest/user_guide.html
index 41df0842b..9226cffc6 100644
--- a/latest/user_guide.html
+++ b/latest/user_guide.html
@@ -1076,8 +1076,8 @@ <h3><a class="toc-backref" href="#id25" role="doc-backlink">Monitoring operation
 <span class="gp">   ....: </span>    <span class="n">ac</span> <span class="o">=</span> <span class="n">sg</span><span class="o">.</span><span class="n">count_variant_alleles</span><span class="p">(</span><span class="n">ds</span><span class="p">)</span><span class="o">.</span><span class="n">variant_allele_count</span><span class="o">.</span><span class="n">compute</span><span class="p">()</span>
 <span class="gp">   ....: </span>
 
-<span class="go">[                                        ] | 0% Completed | 222.57 us</span>
-<span class="go">[########################################] | 100% Completed | 100.50 ms</span>
+<span class="go">[                                        ] | 0% Completed | 165.96 us</span>
+<span class="go">[########################################] | 100% Completed | 100.38 ms</span>
 
 <span class="gp">In [39]: </span><span class="n">ac</span><span class="p">[:</span><span class="mi">5</span><span class="p">]</span>
 <span class="gh">Out[39]: </span>