diff --git a/latest/_sources/changelog.rst.txt b/latest/_sources/changelog.rst.txt index 44853cefe..a5263767f 100644 --- a/latest/_sources/changelog.rst.txt +++ b/latest/_sources/changelog.rst.txt @@ -26,8 +26,11 @@ New Features .. Bug fixes .. ~~~~~~~~~ -.. Documentation -.. ~~~~~~~~~~~~~ +Documentation +~~~~~~~~~~~~~ + +- Update GWAS tutorial to use ``vcf2zarr``. + (:user:`tomwhite`, :pr:`1258`, :issue:`1257`) .. _changelog.0.9.0: diff --git a/latest/_sources/examples/gwas_tutorial.ipynb.txt b/latest/_sources/examples/gwas_tutorial.ipynb.txt index ad8fee564..b0d45f25f 100644 --- a/latest/_sources/examples/gwas_tutorial.ipynb.txt +++ b/latest/_sources/examples/gwas_tutorial.ipynb.txt @@ -25,8 +25,7 @@ "metadata": {}, "outputs": [], "source": [ - "import sgkit as sg\n", - "from sgkit.io.vcf import vcf_to_zarr" + "import sgkit as sg" ] }, { @@ -79,8 +78,12 @@ "import requests\n", "\n", "if not Path(\"1kg.vcf.bgz\").exists():\n", - " response = requests.get(\"https://storage.googleapis.com/sgkit-gwas-tutorial/1kg.vcf.bgz\")\n", + " response = requests.get(\"https://storage.googleapis.com/sgkit-data/tutorial/1kg.vcf.bgz\")\n", " with open(\"1kg.vcf.bgz\", \"wb\") as f:\n", + " f.write(response.content)\n", + "if not Path(\"1kg.vcf.bgz.tbi\").exists():\n", + " response = requests.get(\"https://storage.googleapis.com/sgkit-data/tutorial/1kg.vcf.bgz.tbi\")\n", + " with open(\"1kg.vcf.bgz.tbi\", \"wb\") as f:\n", " f.write(response.content)" ] }, @@ -97,27 +100,33 @@ "id": "elementary-college", "metadata": {}, "source": [ - "Next, [convert it to Zarr](https://sgkit-dev.github.io/sgkit/latest/user_guide.html#converting-genetic-data-to-zarr), stored on the local filesystem in a directory called _1kg.zarr_." + "Next, convert the VCF file to Zarr using the `vcf2zarr` command in [bio2zarr](https://sgkit-dev.github.io/bio2zarr/), stored on the local filesystem in a directory called _1kg.vcz_." ] }, { "cell_type": "code", "execution_count": 4, - "id": "composed-injury", + "id": "78effc1d-b45e-4af5-85ae-e0e7a40ca049", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "[W::bcf_hdr_check_sanity] PL should be declared as Number=G\n" + " Scan: 0%| | 0.00/1.00 [00:00 1kg.schema.json # then edit 1kg.schema.json by hand\n", + "vcf2zarr encode --force -s 1kg.schema.json 1kg.icf 1kg.vcz" ] }, { @@ -125,7 +134,11 @@ "id": "plastic-running", "metadata": {}, "source": [ - "We passed a few arguments to the `vcf_to_zarr` conversion function, so it only converts the first alternate allele (`max_alt_alleles=1`), and to load extra VCF fields we are interested in (`GT`, `DP`, `GQ`, and `AD`). Also, `AD` needed defining as having a `Number` definition of `R` (one value for each allele, including the reference), since the dataset we are using defines it as `.` which means \"unknown\".\n", + "We used the `vcf2zarr explode` command to first convert the VCF to an \"intermediate columnar format\" (ICF), then the `vcf2zarr encode` command to convert the ICF to Zarr, which by convention is stored in a directory with a `vcz` extension.\n", + "\n", + "Note that we specified a JSON schema file that was created with the `vcf2zarr mkschema` command (commented out above), then edited to drop some fields that are not needed for this tutorial (such as `FORMAT/PL`). It was also updated to change the `call_AD` field's third dimension to be `alleles`, which was not set by `vcf2zarr` since the dataset we are using defines `FORMAT/AD` as `.` which means \"unknown\", rather than `R`.\n", + "\n", + "For more information about using `vcf2zarr`, see the tutorial in the [bio2zarr documentation](https://sgkit-dev.github.io/bio2zarr/).\n", "\n", "Now the data has been written as Zarr, all downstream operations on will be much faster. Note that sgkit uses an [Xarray](http://xarray.pydata.org/en/stable/) dataset to represent the VCF data, where Hail uses MatrixTable." ] @@ -137,7 +150,7 @@ "metadata": {}, "outputs": [], "source": [ - "ds = sg.load_dataset(\"1kg.zarr\")" + "ds = sg.load_dataset(\"1kg.vcz\")" ] }, { @@ -198,6 +211,7 @@ "}\n", "\n", "html[theme=dark],\n", + "html[data-theme=dark],\n", "body[data-theme=dark],\n", "body.vscode-dark {\n", " --xr-font-color0: rgba(255, 255, 255, 1);\n", @@ -428,6 +442,11 @@ " grid-column: 4;\n", "}\n", "\n", + ".xr-index-preview {\n", + " grid-column: 2 / 5;\n", + " color: var(--xr-font-color2);\n", + "}\n", + "\n", ".xr-var-name,\n", ".xr-var-dims,\n", ".xr-var-dtype,\n", @@ -449,14 +468,16 @@ "}\n", "\n", ".xr-var-attrs,\n", - ".xr-var-data {\n", + ".xr-var-data,\n", + ".xr-index-data {\n", " display: none;\n", " background-color: var(--xr-background-color) !important;\n", " padding-bottom: 5px !important;\n", "}\n", "\n", ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", - ".xr-var-data-in:checked ~ .xr-var-data {\n", + ".xr-var-data-in:checked ~ .xr-var-data,\n", + ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", @@ -466,13 +487,16 @@ "\n", ".xr-var-name span,\n", ".xr-var-data,\n", + ".xr-index-name div,\n", + ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", - ".xr-var-data {\n", + ".xr-var-data,\n", + ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", @@ -510,7 +534,8 @@ "}\n", "\n", ".xr-icon-database,\n", - ".xr-icon-file-text2 {\n", + ".xr-icon-file-text2,\n", + ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", @@ -519,26 +544,26 @@ " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", - "
<xarray.Dataset>\n",
+       "
<xarray.Dataset> Size: 28MB\n",
        "Dimensions:               (variants: 10879, samples: 284, alleles: 2,\n",
        "                           ploidy: 2, contigs: 84, filters: 1)\n",
        "Dimensions without coordinates: variants, samples, alleles, ploidy, contigs,\n",
        "                                filters\n",
        "Data variables: (12/17)\n",
-       "    call_AD               (variants, samples, alleles) int32 dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
-       "    call_DP               (variants, samples) int32 dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
-       "    call_GQ               (variants, samples) int32 dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
-       "    call_genotype         (variants, samples, ploidy) int8 dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
-       "    call_genotype_mask    (variants, samples, ploidy) bool dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
-       "    call_genotype_phased  (variants, samples) bool dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
+       "    call_AD               (variants, samples, alleles) int8 6MB dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
+       "    call_DP               (variants, samples) int8 3MB dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
+       "    call_GQ               (variants, samples) int8 3MB dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
+       "    call_genotype         (variants, samples, ploidy) int8 6MB dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
+       "    call_genotype_mask    (variants, samples, ploidy) bool 6MB dask.array<chunksize=(10000, 284, 2), meta=np.ndarray>\n",
+       "    call_genotype_phased  (variants, samples) bool 3MB dask.array<chunksize=(10000, 284), meta=np.ndarray>\n",
        "    ...                    ...\n",
-       "    variant_contig        (variants) int8 dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_filter        (variants, filters) bool dask.array<chunksize=(10000, 1), meta=np.ndarray>\n",
-       "    variant_id            (variants) object dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_id_mask       (variants) bool dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_position      (variants) int32 dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "    variant_quality       (variants) float32 dask.array<chunksize=(10000,), meta=np.ndarray>\n",
-       "Attributes: (7)
  • parents
    PandasIndex
    PandasIndex(Index(['SIRE', 'DAM'], dtype='object', name='parents'))

    • Note that the index column of the pedigree dataframe (containing the sample IDs) has been translated to coordinates for the “samples” dimension of the data array. Likewise, the column names have been used as coordinates of the “parents” dimension.

    @@ -1263,7 +1263,7 @@

    Reading pedigree dataReading pedigree dataReading pedigree dataReading pedigree data + dtype='object', name='samples', length=6473))
  • parents
    PandasIndex
    PandasIndex(Index(['SIRE', 'DAM'], dtype='object', name='parents'))
    • @@ -1663,7 +1668,7 @@

    Working with pedigree dataparent_id 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 parent matrix contains integer indices of the parent samples within the dataset allowing for fast numerical calculations. @@ -2080,7 +2090,7 @@

    Pedigree relationshipsPedigree relationshipsPedigree relationshipsPedigree relationships

    Note that the dimensions of the matrices are called samples_0 and samples_1 to avoid using a single dimension twice in an xarray DataArray. Unfortunately, this means that the coordinates of the samples array have not been propagated to the new dimensions. @@ -2527,7 +2542,7 @@

    Pedigree relationshipsPedigree relationshipsPedigree relationshipsPedigree relationships + dtype='object', name='samples_1', length=6473))
  • comment :
    Relationship matrix derived from pedigree structure.

    • We can plot the relationship using matplotlib.

    @@ -3167,7 +3187,7 @@

    Genomic relationshipsGenomic relationshipsGenomic relationshipsGenomic relationships + dtype='object', name='samples', length=3534))

    • Next we create a dataset containing the call_dosage and sample_id variables.

    @@ -3567,7 +3592,7 @@

    Genomic relationshipsGenomic relationshipsGenomic relationshipsGenomic relationships + dtype='object', name='variants', length=1000))

    • @@ -3951,7 +3981,7 @@

    The VanRaden GRM -
    /tmp/ipykernel_2721/892134664.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`.
+
    /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`.
   tril_idx = np.tril_indices(gen.dims["samples"])
 
    
 
    
@@ -4055,7 +4085,7 @@ 
    A better estimate of ancestral allele frequencies
    -
    /tmp/ipykernel_2721/3477141311.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`.
+
    /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`.
   tril_idx = np.tril_indices(gen.dims["samples"])
 
    
 
    
@@ -4127,7 +4157,7 @@ 
    Weir-Goudet GRM
-
    /tmp/ipykernel_2721/70656024.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`.
+
    /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`.
   tril_idx = np.tril_indices(gen.dims["samples"])
 
    
 
    
@@ -4255,8 +4285,7 @@ 
    References
-  
-  
+   
 
    
 
                 
diff --git a/latest/generated/sgkit.Fst.html b/latest/generated/sgkit.Fst.html
index 323a50b69..5a6e4d7e7 100644
--- a/latest/generated/sgkit.Fst.html
+++ b/latest/generated/sgkit.Fst.html
@@ -56,13 +56,9 @@
     
     
     
-    
-
+     
   
-  
-
-
-
+     
   
   
   
@@ -743,8 +739,7 @@
                 
 
                 
    
 
                 
diff --git a/latest/generated/sgkit.Garud_H.html b/latest/generated/sgkit.Garud_H.html
index 689e67273..443994e85 100644
--- a/latest/generated/sgkit.Garud_H.html
+++ b/latest/generated/sgkit.Garud_H.html
@@ -56,13 +56,9 @@
     
     
     
-    
-
+     
   
-  
-
-
-
+     
   
   
   
@@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.Tajimas_D.html b/latest/generated/sgkit.Tajimas_D.html index 797d432e7..7a99e6e44 100644 --- a/latest/generated/sgkit.Tajimas_D.html +++ b/latest/generated/sgkit.Tajimas_D.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.Weir_Goudet_beta.html b/latest/generated/sgkit.Weir_Goudet_beta.html index a4eb34121..345594dd4 100644 --- a/latest/generated/sgkit.Weir_Goudet_beta.html +++ b/latest/generated/sgkit.Weir_Goudet_beta.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@ diff --git a/latest/generated/sgkit.call_allele_frequencies.html b/latest/generated/sgkit.call_allele_frequencies.html index 8993da7b8..23d5b4485 100644 --- a/latest/generated/sgkit.call_allele_frequencies.html +++ b/latest/generated/sgkit.call_allele_frequencies.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.cohort_allele_frequencies.html b/latest/generated/sgkit.cohort_allele_frequencies.html index d986ef0b8..5139653d8 100644 --- a/latest/generated/sgkit.cohort_allele_frequencies.html +++ b/latest/generated/sgkit.cohort_allele_frequencies.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    diff --git a/latest/generated/sgkit.convert_call_to_index.html b/latest/generated/sgkit.convert_call_to_index.html index 9dbeefc5a..f7d920eb4 100644 --- a/latest/generated/sgkit.convert_call_to_index.html +++ b/latest/generated/sgkit.convert_call_to_index.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.convert_probability_to_call.html b/latest/generated/sgkit.convert_probability_to_call.html index be9db18fa..cee2f286a 100644 --- a/latest/generated/sgkit.convert_probability_to_call.html +++ b/latest/generated/sgkit.convert_probability_to_call.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.count_call_alleles.html b/latest/generated/sgkit.count_call_alleles.html index b534a8a2b..88ff74cf0 100644 --- a/latest/generated/sgkit.count_call_alleles.html +++ b/latest/generated/sgkit.count_call_alleles.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.count_cohort_alleles.html b/latest/generated/sgkit.count_cohort_alleles.html index 8952bcafb..4c204c0c5 100644 --- a/latest/generated/sgkit.count_cohort_alleles.html +++ b/latest/generated/sgkit.count_cohort_alleles.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.count_variant_alleles.html b/latest/generated/sgkit.count_variant_alleles.html index 259a66d5e..412979884 100644 --- a/latest/generated/sgkit.count_variant_alleles.html +++ b/latest/generated/sgkit.count_variant_alleles.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.count_variant_alleles#

    @@ -765,7 +760,7 @@

    sgkit.count_variant_allelesds, it will be computed using count_call_alleles().

    -
    using Literal['call_allele_count', 'call_genotype'] (default: 'call_allele_count')

    specify the variable used to calculate allele counts from. +

    using {‘call_allele_count’, ‘call_genotype’}Literal['call_allele_count', 'call_genotype'] (default: 'call_allele_count')

    specify the variable used to calculate allele counts from. If 'call_allele_count' (the default), the result will be calculated from the call_allele_count variable. If 'call_genotype', the result will be calculated from @@ -819,8 +814,7 @@

    sgkit.count_variant_alleles - - +

    diff --git a/latest/generated/sgkit.count_variant_genotypes.html b/latest/generated/sgkit.count_variant_genotypes.html index fbe62abc1..6cc7a1a9b 100644 --- a/latest/generated/sgkit.count_variant_genotypes.html +++ b/latest/generated/sgkit.count_variant_genotypes.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.display_genotypes.html b/latest/generated/sgkit.display_genotypes.html index cdf76cc11..87201e1ba 100644 --- a/latest/generated/sgkit.display_genotypes.html +++ b/latest/generated/sgkit.display_genotypes.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.display_pedigree.html b/latest/generated/sgkit.display_pedigree.html index 783c73ca9..5b3e0b818 100644 --- a/latest/generated/sgkit.display_pedigree.html +++ b/latest/generated/sgkit.display_pedigree.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.divergence.html b/latest/generated/sgkit.divergence.html index 099f25f90..b0ccc45c7 100644 --- a/latest/generated/sgkit.divergence.html +++ b/latest/generated/sgkit.divergence.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.diversity.html b/latest/generated/sgkit.diversity.html index e43537f3d..9493d9ca6 100644 --- a/latest/generated/sgkit.diversity.html +++ b/latest/generated/sgkit.diversity.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.filter_partial_calls.html b/latest/generated/sgkit.filter_partial_calls.html index 3207a8f63..2b3bfb967 100644 --- a/latest/generated/sgkit.filter_partial_calls.html +++ b/latest/generated/sgkit.filter_partial_calls.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.genee.html b/latest/generated/sgkit.genee.html index 1226e2a31..2276999a1 100644 --- a/latest/generated/sgkit.genee.html +++ b/latest/generated/sgkit.genee.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.genomic_relationship.html b/latest/generated/sgkit.genomic_relationship.html index e4df6c8f3..c02596016 100644 --- a/latest/generated/sgkit.genomic_relationship.html +++ b/latest/generated/sgkit.genomic_relationship.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.genomic_relationship#

    @@ -766,7 +761,7 @@

    sgkit.genomic_relationshipHashable (default: 'call_dosage')

    Input variable name holding call_dosage as defined by sgkit.variables.call_dosage_spec.

    -
    estimator Literal['VanRaden', 'Endelman-Jannink'] | NoneOptional[Literal['VanRaden', 'Endelman-Jannink']] (default: None)

    Specifies the relatedness estimator to use. Must be one of +

    estimator {‘VanRaden’, ‘Endelman-Jannink’} | NoneOptional[Literal['VanRaden', 'Endelman-Jannink']] (default: None)

    Specifies the relatedness estimator to use. Must be one of 'VanRaden' (the default) or 'Endelman-Jannink'.

    ancestral_frequency Hashable | NoneOptional[Hashable] (default: None)

    Frequency of variant alleles corresponding to call_dosage within @@ -946,8 +941,7 @@

    sgkit.genomic_relationship - - +

    diff --git a/latest/generated/sgkit.gwas_linear_regression.html b/latest/generated/sgkit.gwas_linear_regression.html index 3fa446e30..619b0e44d 100644 --- a/latest/generated/sgkit.gwas_linear_regression.html +++ b/latest/generated/sgkit.gwas_linear_regression.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.hardy_weinberg_test.html b/latest/generated/sgkit.hardy_weinberg_test.html index ea33c1cf7..f3eee2b1e 100644 --- a/latest/generated/sgkit.hardy_weinberg_test.html +++ b/latest/generated/sgkit.hardy_weinberg_test.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.hybrid_inverse_relationship.html b/latest/generated/sgkit.hybrid_inverse_relationship.html index e55d65a08..0e331931f 100644 --- a/latest/generated/sgkit.hybrid_inverse_relationship.html +++ b/latest/generated/sgkit.hybrid_inverse_relationship.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@
    - -
    +

    sgkit.hybrid_inverse_relationship#

    @@ -775,7 +770,7 @@

    sgkit.hybrid_inverse_relationshipLiteral['Martini'] | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option +

    estimator {‘Martini’} | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option is "Martini" following Martini et al 2018 [1] which expands on the estimators of Legarra et al 2009 [2] and Aguiler et al 2010 [3].

    @@ -900,8 +895,7 @@

    sgkit.hybrid_inverse_relationship - - +

    diff --git a/latest/generated/sgkit.hybrid_relationship.html b/latest/generated/sgkit.hybrid_relationship.html index 61ac2b45d..4b24e0e3a 100644 --- a/latest/generated/sgkit.hybrid_relationship.html +++ b/latest/generated/sgkit.hybrid_relationship.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@
    - -
    +

    sgkit.hybrid_relationship#

    @@ -778,7 +773,7 @@

    sgkit.hybrid_relationshipLiteral['Martini'] | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option +

    estimator {‘Martini’} | NoneOptional[Literal['Martini']] (default: None)

    Specifies the estimator used to combine matrices. Currently the only option is "Martini" following Martini et al 2018 [1] which expands on the estimators of Legarra et al 2009 [2] and Aguiler et al 2010 [3].

    @@ -884,8 +879,7 @@

    sgkit.hybrid_relationship - - +

    diff --git a/latest/generated/sgkit.identity_by_state.html b/latest/generated/sgkit.identity_by_state.html index 1a9f5f755..6f79de54e 100644 --- a/latest/generated/sgkit.identity_by_state.html +++ b/latest/generated/sgkit.identity_by_state.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.identity_by_state#

    @@ -770,7 +765,7 @@

    sgkit.identity_by_stateds, it will be computed using call_allele_frequencies().

    -
    method Literal['frequencies', 'matching'] (default: 'frequencies')

    The method used for IBS estimation. Defaults to “frequencies” +

    method {‘frequencies’, ‘matching’}Literal['frequencies', 'matching'] (default: 'frequencies')

    The method used for IBS estimation. Defaults to “frequencies” which calculates IBS probabilities by matrix multiplication of call allele frequencies which is more efficient when the alleles dimension is small. @@ -818,8 +813,7 @@

    sgkit.identity_by_state
    - - +

    diff --git a/latest/generated/sgkit.individual_heterozygosity.html b/latest/generated/sgkit.individual_heterozygosity.html index 66f0dafe2..58f4c5ac0 100644 --- a/latest/generated/sgkit.individual_heterozygosity.html +++ b/latest/generated/sgkit.individual_heterozygosity.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.infer_call_ploidy.html b/latest/generated/sgkit.infer_call_ploidy.html index 96c427992..a0d3eb2c8 100644 --- a/latest/generated/sgkit.infer_call_ploidy.html +++ b/latest/generated/sgkit.infer_call_ploidy.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.infer_sample_ploidy.html b/latest/generated/sgkit.infer_sample_ploidy.html index c8fdb7e21..0cf1d1f9c 100644 --- a/latest/generated/sgkit.infer_sample_ploidy.html +++ b/latest/generated/sgkit.infer_sample_ploidy.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.infer_variant_ploidy.html b/latest/generated/sgkit.infer_variant_ploidy.html index 57d0aecfa..01b23a980 100644 --- a/latest/generated/sgkit.infer_variant_ploidy.html +++ b/latest/generated/sgkit.infer_variant_ploidy.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.invert_relationship_matrix.html b/latest/generated/sgkit.invert_relationship_matrix.html index 4f3579ce8..af39f7d13 100644 --- a/latest/generated/sgkit.invert_relationship_matrix.html +++ b/latest/generated/sgkit.invert_relationship_matrix.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.bgen.bgen_to_zarr.html b/latest/generated/sgkit.io.bgen.bgen_to_zarr.html index 1e3f8eaee..d086397ab 100644 --- a/latest/generated/sgkit.io.bgen.bgen_to_zarr.html +++ b/latest/generated/sgkit.io.bgen.bgen_to_zarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.bgen.read_bgen.html b/latest/generated/sgkit.io.bgen.read_bgen.html index a5c917c99..f192c3745 100644 --- a/latest/generated/sgkit.io.bgen.read_bgen.html +++ b/latest/generated/sgkit.io.bgen.read_bgen.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.bgen.rechunk_bgen.html b/latest/generated/sgkit.io.bgen.rechunk_bgen.html index 12cf1c78e..6e7f7b267 100644 --- a/latest/generated/sgkit.io.bgen.rechunk_bgen.html +++ b/latest/generated/sgkit.io.bgen.rechunk_bgen.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.plink_to_zarr.html b/latest/generated/sgkit.io.plink.plink_to_zarr.html index 6f8d9697a..5f1e097fa 100644 --- a/latest/generated/sgkit.io.plink.plink_to_zarr.html +++ b/latest/generated/sgkit.io.plink.plink_to_zarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.read_plink.html b/latest/generated/sgkit.io.plink.read_plink.html index 3ae50fa9b..197d77090 100644 --- a/latest/generated/sgkit.io.plink.read_plink.html +++ b/latest/generated/sgkit.io.plink.read_plink.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.write_plink.html b/latest/generated/sgkit.io.plink.write_plink.html index 51ae1dd7c..fc9f72e8d 100644 --- a/latest/generated/sgkit.io.plink.write_plink.html +++ b/latest/generated/sgkit.io.plink.write_plink.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.plink.zarr_to_plink.html b/latest/generated/sgkit.io.plink.zarr_to_plink.html index beaca87c9..6bf6eae2d 100644 --- a/latest/generated/sgkit.io.plink.zarr_to_plink.html +++ b/latest/generated/sgkit.io.plink.zarr_to_plink.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.concat_zarrs.html b/latest/generated/sgkit.io.vcf.concat_zarrs.html index 5004eb90a..43c0e5caa 100644 --- a/latest/generated/sgkit.io.vcf.concat_zarrs.html +++ b/latest/generated/sgkit.io.vcf.concat_zarrs.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.partition_into_regions.html b/latest/generated/sgkit.io.vcf.partition_into_regions.html index da03d6fe2..7829f0778 100644 --- a/latest/generated/sgkit.io.vcf.partition_into_regions.html +++ b/latest/generated/sgkit.io.vcf.partition_into_regions.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.read_vcf.html b/latest/generated/sgkit.io.vcf.read_vcf.html index 24477ed72..8cb0d94d6 100644 --- a/latest/generated/sgkit.io.vcf.read_vcf.html +++ b/latest/generated/sgkit.io.vcf.read_vcf.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.vcf_to_zarr.html b/latest/generated/sgkit.io.vcf.vcf_to_zarr.html index 2370dfe9e..5fa2192f7 100644 --- a/latest/generated/sgkit.io.vcf.vcf_to_zarr.html +++ b/latest/generated/sgkit.io.vcf.vcf_to_zarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html b/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html index 72baf1772..216e8c75b 100644 --- a/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html +++ b/latest/generated/sgkit.io.vcf.vcf_to_zarrs.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.write_vcf.html b/latest/generated/sgkit.io.vcf.write_vcf.html index 68f62feb0..d74b32b9a 100644 --- a/latest/generated/sgkit.io.vcf.write_vcf.html +++ b/latest/generated/sgkit.io.vcf.write_vcf.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.zarr_array_sizes.html b/latest/generated/sgkit.io.vcf.zarr_array_sizes.html index 8fbd1b11c..58445713f 100644 --- a/latest/generated/sgkit.io.vcf.zarr_array_sizes.html +++ b/latest/generated/sgkit.io.vcf.zarr_array_sizes.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.io.vcf.zarr_to_vcf.html b/latest/generated/sgkit.io.vcf.zarr_to_vcf.html index ef4bb749e..9518723c4 100644 --- a/latest/generated/sgkit.io.vcf.zarr_to_vcf.html +++ b/latest/generated/sgkit.io.vcf.zarr_to_vcf.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.ld_matrix.html b/latest/generated/sgkit.ld_matrix.html index 14f96c745..e013fbccb 100644 --- a/latest/generated/sgkit.ld_matrix.html +++ b/latest/generated/sgkit.ld_matrix.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.ld_prune.html b/latest/generated/sgkit.ld_prune.html index 2a85a604d..eac23f876 100644 --- a/latest/generated/sgkit.ld_prune.html +++ b/latest/generated/sgkit.ld_prune.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.load_dataset.html b/latest/generated/sgkit.load_dataset.html index fb3fca649..b8de7fdee 100644 --- a/latest/generated/sgkit.load_dataset.html +++ b/latest/generated/sgkit.load_dataset.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.maximal_independent_set.html b/latest/generated/sgkit.maximal_independent_set.html index dd17988f1..4ddb5d299 100644 --- a/latest/generated/sgkit.maximal_independent_set.html +++ b/latest/generated/sgkit.maximal_independent_set.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.observed_heterozygosity.html b/latest/generated/sgkit.observed_heterozygosity.html index c7b674799..de1f0a1a8 100644 --- a/latest/generated/sgkit.observed_heterozygosity.html +++ b/latest/generated/sgkit.observed_heterozygosity.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pairwise_distance.html b/latest/generated/sgkit.pairwise_distance.html index 261a859a6..1b8cf889f 100644 --- a/latest/generated/sgkit.pairwise_distance.html +++ b/latest/generated/sgkit.pairwise_distance.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pairwise_distance#

    @@ -781,7 +776,7 @@

    sgkit.pairwise_distance -
    metric Literal['euclidean', 'correlation'] (default: 'euclidean')

    The distance metric to use. The distance function can be +

    metric {‘euclidean’, ‘correlation’}Literal['euclidean', 'correlation'] (default: 'euclidean')

    The distance metric to use. The distance function can be ‘euclidean’ or ‘correlation’.

    split_every int | NoneOptional[int] (default: None)

    Determines the depth of the recursive aggregation in the reduction @@ -791,7 +786,7 @@

    sgkit.pairwise_distance

    -
    device Literal['cpu', 'gpu'] (default: 'cpu')

    The architecture to run the calculation on, either of “cpu” or “gpu”

    +
    device {‘cpu’, ‘gpu’}Literal['cpu', 'gpu'] (default: 'cpu')

    The architecture to run the calculation on, either of “cpu” or “gpu”

    @@ -838,8 +833,7 @@

    sgkit.pairwise_distance
    - - +

    diff --git a/latest/generated/sgkit.parent_indices.html b/latest/generated/sgkit.parent_indices.html index 82cc66ecf..0aeda1fc3 100644 --- a/latest/generated/sgkit.parent_indices.html +++ b/latest/generated/sgkit.parent_indices.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pbs.html b/latest/generated/sgkit.pbs.html index 71a761c6a..62ab3379d 100644 --- a/latest/generated/sgkit.pbs.html +++ b/latest/generated/sgkit.pbs.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pc_relate.html b/latest/generated/sgkit.pc_relate.html index c9871a224..f40629432 100644 --- a/latest/generated/sgkit.pc_relate.html +++ b/latest/generated/sgkit.pc_relate.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.pedigree_contribution.html b/latest/generated/sgkit.pedigree_contribution.html index 1e4774143..37b495b74 100644 --- a/latest/generated/sgkit.pedigree_contribution.html +++ b/latest/generated/sgkit.pedigree_contribution.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pedigree_contribution#

    @@ -756,7 +751,7 @@

    sgkit.pedigree_contribution
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['even', 'variable'] (default: 'even')

    The method used for estimating genomic contributions. +

    method {‘even’, ‘variable’}Literal['even', 'variable'] (default: 'even')

    The method used for estimating genomic contributions. The ‘even’ method assumes that all samples are of a single, even ploidy (e.g., diploid) and have even contributions from each parent. The ‘variable’ method allows for un-even @@ -831,8 +826,7 @@

    sgkit.pedigree_contribution - - +

    diff --git a/latest/generated/sgkit.pedigree_inbreeding.html b/latest/generated/sgkit.pedigree_inbreeding.html index 4acf32d40..f312e0438 100644 --- a/latest/generated/sgkit.pedigree_inbreeding.html +++ b/latest/generated/sgkit.pedigree_inbreeding.html @@ -58,13 +58,9 @@ - - + - - - - + @@ -745,8 +741,7 @@
    - -
    +

    sgkit.pedigree_inbreeding#

    @@ -757,7 +752,7 @@

    sgkit.pedigree_inbreeding
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for inbreeding estimation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’}Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for inbreeding estimation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -915,8 +910,7 @@

    sgkit.pedigree_inbreeding - - +

    diff --git a/latest/generated/sgkit.pedigree_inverse_kinship.html b/latest/generated/sgkit.pedigree_inverse_kinship.html index 89cf61c4d..ce274f679 100644 --- a/latest/generated/sgkit.pedigree_inverse_kinship.html +++ b/latest/generated/sgkit.pedigree_inverse_kinship.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pedigree_inverse_kinship#

    @@ -757,7 +752,7 @@

    sgkit.pedigree_inverse_kinship
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’}Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -928,8 +923,7 @@

    sgkit.pedigree_inverse_kinship - - +

    diff --git a/latest/generated/sgkit.pedigree_kinship.html b/latest/generated/sgkit.pedigree_kinship.html index 24fe3a66a..876715c3b 100644 --- a/latest/generated/sgkit.pedigree_kinship.html +++ b/latest/generated/sgkit.pedigree_kinship.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.pedigree_kinship#

    @@ -757,7 +752,7 @@

    sgkit.pedigree_kinship
    ds Dataset

    Dataset containing pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’}Literal['diploid', 'Hamilton-Kerr'] (default: 'diploid')

    The method used for kinship estimation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -996,8 +991,7 @@

    sgkit.pedigree_kinship
    - - +

    diff --git a/latest/generated/sgkit.pedigree_sel.html b/latest/generated/sgkit.pedigree_sel.html index a355f3ab8..62f15ce40 100644 --- a/latest/generated/sgkit.pedigree_sel.html +++ b/latest/generated/sgkit.pedigree_sel.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.read_scikit_allel_vcfzarr.html b/latest/generated/sgkit.read_scikit_allel_vcfzarr.html index b93029e03..0911b8037 100644 --- a/latest/generated/sgkit.read_scikit_allel_vcfzarr.html +++ b/latest/generated/sgkit.read_scikit_allel_vcfzarr.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.regenie.html b/latest/generated/sgkit.regenie.html index 3ea2f144f..70fc0b4d5 100644 --- a/latest/generated/sgkit.regenie.html +++ b/latest/generated/sgkit.regenie.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.sample_stats.html b/latest/generated/sgkit.sample_stats.html index fa95cefca..2f140eac7 100644 --- a/latest/generated/sgkit.sample_stats.html +++ b/latest/generated/sgkit.sample_stats.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.save_dataset.html b/latest/generated/sgkit.save_dataset.html index ddc50fcbd..09843fbc3 100644 --- a/latest/generated/sgkit.save_dataset.html +++ b/latest/generated/sgkit.save_dataset.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.simulate_genedrop.html b/latest/generated/sgkit.simulate_genedrop.html index 312b4506c..f4c99b83c 100644 --- a/latest/generated/sgkit.simulate_genedrop.html +++ b/latest/generated/sgkit.simulate_genedrop.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.simulate_genedrop#

    @@ -758,7 +753,7 @@

    sgkit.simulate_genedrop
    ds Dataset

    Dataset containing genotype calls and pedigree structure.

    -
    method Literal['diploid', 'Hamilton-Kerr'] | NoneOptional[Literal['diploid', 'Hamilton-Kerr']] (default: 'diploid')

    The method used for gene-drop simulation. Defaults to “diploid” +

    method {‘diploid’, ‘Hamilton-Kerr’} | NoneOptional[Literal['diploid', 'Hamilton-Kerr']] (default: 'diploid')

    The method used for gene-drop simulation. Defaults to “diploid” which is only suitable for pedigrees in which all samples are diploids resulting from sexual reproduction. The “Hamilton-Kerr” method is suitable for autopolyploid and @@ -893,8 +888,7 @@

    sgkit.simulate_genedrop
    - - +

    diff --git a/latest/generated/sgkit.simulate_genotype_call_dataset.html b/latest/generated/sgkit.simulate_genotype_call_dataset.html index 15b5bbf9d..717b14489 100644 --- a/latest/generated/sgkit.simulate_genotype_call_dataset.html +++ b/latest/generated/sgkit.simulate_genotype_call_dataset.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_allele_count_spec.html b/latest/generated/sgkit.variables.call_allele_count_spec.html index a8f2aafd9..79ab096e6 100644 --- a/latest/generated/sgkit.variables.call_allele_count_spec.html +++ b/latest/generated/sgkit.variables.call_allele_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_allele_frequency_spec.html b/latest/generated/sgkit.variables.call_allele_frequency_spec.html index b80c2d25d..650e8c025 100644 --- a/latest/generated/sgkit.variables.call_allele_frequency_spec.html +++ b/latest/generated/sgkit.variables.call_allele_frequency_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_dosage_mask_spec.html b/latest/generated/sgkit.variables.call_dosage_mask_spec.html index b2a3c7306..308c9ac6d 100644 --- a/latest/generated/sgkit.variables.call_dosage_mask_spec.html +++ b/latest/generated/sgkit.variables.call_dosage_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_dosage_spec.html b/latest/generated/sgkit.variables.call_dosage_spec.html index 6146bde64..870c7cdfa 100644 --- a/latest/generated/sgkit.variables.call_dosage_spec.html +++ b/latest/generated/sgkit.variables.call_dosage_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.call_dosage_spec#

    -sgkit.variables.call_dosage_spec = ArrayLikeSpec(default_name='call_dosage', __doc__='\nDosages, encoded as floats, with NaN indicating a missing value.\nDosages can represent one of several possible quantities, e.g.:\n- Alternate allele counts\n- Recessive or dominant allele encodings\n- True dosages as computed from imputed or probabilistic variant calls\n- Any other custom encoding in a user-defined variable\n', kind={'f', 'i', 'u'}, ndim=2, dims=('variants', 'samples'))#
    +sgkit.variables.call_dosage_spec = ArrayLikeSpec(default_name='call_dosage', __doc__='\nDosages, encoded as floats, with NaN indicating a missing value.\nDosages can represent one of several possible quantities, e.g.:\n- Alternate allele counts\n- Recessive or dominant allele encodings\n- True dosages as computed from imputed or probabilistic variant calls\n- Any other custom encoding in a user-defined variable\n', kind={'u', 'f', 'i'}, ndim=2, dims=('variants', 'samples'))#

    Dosages, encoded as floats, with NaN indicating a missing value. Dosages can represent one of several possible quantities, e.g.: - Alternate allele counts @@ -760,8 +755,7 @@

    sgkit.variables.call_dosage_spec - - +

    diff --git a/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html index b5e17e55d..309f4bdc2 100644 --- a/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_complete_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_complete_spec.html b/latest/generated/sgkit.variables.call_genotype_complete_spec.html index a57c2e7d4..15b46c265 100644 --- a/latest/generated/sgkit.variables.call_genotype_complete_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_complete_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_fill_spec.html b/latest/generated/sgkit.variables.call_genotype_fill_spec.html index f23415c56..94ebbc43f 100644 --- a/latest/generated/sgkit.variables.call_genotype_fill_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_fill_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html index 571a94677..aa1b1fb6d 100644 --- a/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_index_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_index_spec.html b/latest/generated/sgkit.variables.call_genotype_index_spec.html index b743c27a4..d8b350a93 100644 --- a/latest/generated/sgkit.variables.call_genotype_index_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_index_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_mask_spec.html index 5f833c13c..cb0ea4954 100644 --- a/latest/generated/sgkit.variables.call_genotype_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_phased_spec.html b/latest/generated/sgkit.variables.call_genotype_phased_spec.html index db6c919bb..742c8caba 100644 --- a/latest/generated/sgkit.variables.call_genotype_phased_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_phased_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html b/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html index a031ab07b..63f7078c9 100644 --- a/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_probability_mask_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_probability_spec.html b/latest/generated/sgkit.variables.call_genotype_probability_spec.html index 1ab9a4e5f..e7970b9b6 100644 --- a/latest/generated/sgkit.variables.call_genotype_probability_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_probability_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_genotype_spec.html b/latest/generated/sgkit.variables.call_genotype_spec.html index 3b3d75ba8..d8fa063b1 100644 --- a/latest/generated/sgkit.variables.call_genotype_spec.html +++ b/latest/generated/sgkit.variables.call_genotype_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_heterozygosity_spec.html b/latest/generated/sgkit.variables.call_heterozygosity_spec.html index 55c75206a..bdc70106b 100644 --- a/latest/generated/sgkit.variables.call_heterozygosity_spec.html +++ b/latest/generated/sgkit.variables.call_heterozygosity_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.call_ploidy_spec.html b/latest/generated/sgkit.variables.call_ploidy_spec.html index 9817b7cf3..e0898dbea 100644 --- a/latest/generated/sgkit.variables.call_ploidy_spec.html +++ b/latest/generated/sgkit.variables.call_ploidy_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.cohort_allele_count_spec.html b/latest/generated/sgkit.variables.cohort_allele_count_spec.html index 7c8895dac..719f07b85 100644 --- a/latest/generated/sgkit.variables.cohort_allele_count_spec.html +++ b/latest/generated/sgkit.variables.cohort_allele_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html b/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html index c57f54971..eb22e3369 100644 --- a/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html +++ b/latest/generated/sgkit.variables.cohort_allele_frequency_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.covariates_spec.html b/latest/generated/sgkit.variables.covariates_spec.html index 0c8fbf3d2..d42347e57 100644 --- a/latest/generated/sgkit.variables.covariates_spec.html +++ b/latest/generated/sgkit.variables.covariates_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.interval_contig_name_spec.html b/latest/generated/sgkit.variables.interval_contig_name_spec.html index 621533931..e7274f65b 100644 --- a/latest/generated/sgkit.variables.interval_contig_name_spec.html +++ b/latest/generated/sgkit.variables.interval_contig_name_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.interval_contig_name_spec#

    -sgkit.variables.interval_contig_name_spec = ArrayLikeSpec(default_name='interval_contig_name', __doc__='Interval contig name. Must match a contig defined in the ``contigs`` attribute.', kind={'U', 'S', 'O'}, ndim=1, dims=None)#
    +sgkit.variables.interval_contig_name_spec = ArrayLikeSpec(default_name='interval_contig_name', __doc__='Interval contig name. Must match a contig defined in the ``contigs`` attribute.', kind={'S', 'U', 'O'}, ndim=1, dims=None)#

    Interval contig name. Must match a contig defined in the contigs attribute.

    - - +
    diff --git a/latest/generated/sgkit.variables.interval_start_spec.html b/latest/generated/sgkit.variables.interval_start_spec.html index aa8775497..51751067d 100644 --- a/latest/generated/sgkit.variables.interval_start_spec.html +++ b/latest/generated/sgkit.variables.interval_start_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.interval_start_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.interval_start_spec - - +

    diff --git a/latest/generated/sgkit.variables.interval_stop_spec.html b/latest/generated/sgkit.variables.interval_stop_spec.html index ae1f27e35..ff72547a2 100644 --- a/latest/generated/sgkit.variables.interval_stop_spec.html +++ b/latest/generated/sgkit.variables.interval_stop_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html b/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html index 86c6b9b68..f9526f0a9 100644 --- a/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html +++ b/latest/generated/sgkit.variables.ld_prune_index_to_drop_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.parent_id_spec.html b/latest/generated/sgkit.variables.parent_id_spec.html index 292cd9dcd..cf255f734 100644 --- a/latest/generated/sgkit.variables.parent_id_spec.html +++ b/latest/generated/sgkit.variables.parent_id_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.parent_id_spec#

    -sgkit.variables.parent_id_spec = ArrayLikeSpec(default_name='parent_id', __doc__='\nUnique identifiers of parent samples matching those in\n:data:`sgkit.variables.sample_id_spec`.\n', kind={'U', 'S', 'O'}, ndim=2, dims=('samples', 'parents'))#
    +sgkit.variables.parent_id_spec = ArrayLikeSpec(default_name='parent_id', __doc__='\nUnique identifiers of parent samples matching those in\n:data:`sgkit.variables.sample_id_spec`.\n', kind={'S', 'U', 'O'}, ndim=2, dims=('samples', 'parents'))#

    Unique identifiers of parent samples matching those in sgkit.variables.sample_id_spec.

    @@ -756,8 +751,7 @@

    sgkit.variables.parent_id_spec - - +

    diff --git a/latest/generated/sgkit.variables.parent_spec.html b/latest/generated/sgkit.variables.parent_spec.html index 414969887..8c1c1e7d1 100644 --- a/latest/generated/sgkit.variables.parent_spec.html +++ b/latest/generated/sgkit.variables.parent_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.pc_relate_phi_spec.html b/latest/generated/sgkit.variables.pc_relate_phi_spec.html index 0649b17df..ba7d497da 100644 --- a/latest/generated/sgkit.variables.pc_relate_phi_spec.html +++ b/latest/generated/sgkit.variables.pc_relate_phi_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.regenie_base_prediction_spec.html b/latest/generated/sgkit.variables.regenie_base_prediction_spec.html index 89e35d48b..a4f4754e0 100644 --- a/latest/generated/sgkit.variables.regenie_base_prediction_spec.html +++ b/latest/generated/sgkit.variables.regenie_base_prediction_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html b/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html index 4a843eb8c..f59cc6264 100644 --- a/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html +++ b/latest/generated/sgkit.variables.regenie_loco_prediction_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html b/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html index cd3011023..0017b6322 100644 --- a/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html +++ b/latest/generated/sgkit.variables.regenie_meta_prediction_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_call_rate_spec.html b/latest/generated/sgkit.variables.sample_call_rate_spec.html index 833009d73..810a476b0 100644 --- a/latest/generated/sgkit.variables.sample_call_rate_spec.html +++ b/latest/generated/sgkit.variables.sample_call_rate_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_cohort_spec.html b/latest/generated/sgkit.variables.sample_cohort_spec.html index 67b917b09..e0d84fe20 100644 --- a/latest/generated/sgkit.variables.sample_cohort_spec.html +++ b/latest/generated/sgkit.variables.sample_cohort_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_id_spec.html b/latest/generated/sgkit.variables.sample_id_spec.html index 6bc6ff4d0..84f6a555f 100644 --- a/latest/generated/sgkit.variables.sample_id_spec.html +++ b/latest/generated/sgkit.variables.sample_id_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.sample_id_spec#

    -sgkit.variables.sample_id_spec = ArrayLikeSpec(default_name='sample_id', __doc__='The unique identifier of the sample.', kind={'U', 'S', 'O'}, ndim=1, dims=('samples',))#
    +sgkit.variables.sample_id_spec = ArrayLikeSpec(default_name='sample_id', __doc__='The unique identifier of the sample.', kind={'S', 'U', 'O'}, ndim=1, dims=('samples',))#

    The unique identifier of the sample.

    - - +
    diff --git a/latest/generated/sgkit.variables.sample_n_called_spec.html b/latest/generated/sgkit.variables.sample_n_called_spec.html index 7855bc254..0af6d66b6 100644 --- a/latest/generated/sgkit.variables.sample_n_called_spec.html +++ b/latest/generated/sgkit.variables.sample_n_called_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.sample_n_called_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.sample_n_called_spec - - +

    diff --git a/latest/generated/sgkit.variables.sample_n_het_spec.html b/latest/generated/sgkit.variables.sample_n_het_spec.html index 870f917ba..1d52ae58f 100644 --- a/latest/generated/sgkit.variables.sample_n_het_spec.html +++ b/latest/generated/sgkit.variables.sample_n_het_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html b/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html index 9c8e06544..3229d85f0 100644 --- a/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html +++ b/latest/generated/sgkit.variables.sample_n_hom_alt_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html b/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html index f346e465b..4c0ab41e1 100644 --- a/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html +++ b/latest/generated/sgkit.variables.sample_n_hom_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_n_non_ref_spec.html b/latest/generated/sgkit.variables.sample_n_non_ref_spec.html index 712c5d7a0..e5f1536cf 100644 --- a/latest/generated/sgkit.variables.sample_n_non_ref_spec.html +++ b/latest/generated/sgkit.variables.sample_n_non_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_component_spec.html b/latest/generated/sgkit.variables.sample_pca_component_spec.html index 8865b3cee..49dbfc67e 100644 --- a/latest/generated/sgkit.variables.sample_pca_component_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_component_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html b/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html index 3ea20d4c8..c656b31a2 100644 --- a/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html b/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html index 62e1747bc..4ac626ab1 100644 --- a/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_explained_variance_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_loading_spec.html b/latest/generated/sgkit.variables.sample_pca_loading_spec.html index 7c938e0d9..a2fb1d16d 100644 --- a/latest/generated/sgkit.variables.sample_pca_loading_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_loading_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_pca_projection_spec.html b/latest/generated/sgkit.variables.sample_pca_projection_spec.html index ad7ee6d3a..ccbcc3dc4 100644 --- a/latest/generated/sgkit.variables.sample_pca_projection_spec.html +++ b/latest/generated/sgkit.variables.sample_pca_projection_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.sample_ploidy_spec.html b/latest/generated/sgkit.variables.sample_ploidy_spec.html index 9d60e7ea6..96500b348 100644 --- a/latest/generated/sgkit.variables.sample_ploidy_spec.html +++ b/latest/generated/sgkit.variables.sample_ploidy_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Fst_spec.html b/latest/generated/sgkit.variables.stat_Fst_spec.html index a5cf66dd9..bd2faa878 100644 --- a/latest/generated/sgkit.variables.stat_Fst_spec.html +++ b/latest/generated/sgkit.variables.stat_Fst_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_Fst_spec#

    -sgkit.variables.stat_Fst_spec = ArrayLikeSpec(default_name='stat_Fst', __doc__='Fixation index (Fst) between pairs of cohorts.', kind='f', ndim=3, dims=({'variants', 'windows'}, 'cohorts_0', 'cohorts_1'))#
    +sgkit.variables.stat_Fst_spec = ArrayLikeSpec(default_name='stat_Fst', __doc__='Fixation index (Fst) between pairs of cohorts.', kind='f', ndim=3, dims=({'windows', 'variants'}, 'cohorts_0', 'cohorts_1'))#

    Fixation index (Fst) between pairs of cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_Garud_h123_spec.html b/latest/generated/sgkit.variables.stat_Garud_h123_spec.html index a7264f5e5..78d6b0b27 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h123_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h123_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_Garud_h123_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.stat_Garud_h123_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_Garud_h12_spec.html b/latest/generated/sgkit.variables.stat_Garud_h12_spec.html index 2c539d2d4..341ca38c8 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h12_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h12_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Garud_h1_spec.html b/latest/generated/sgkit.variables.stat_Garud_h1_spec.html index e550af086..b43c293e0 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h1_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h1_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html b/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html index 0012fd0a8..d527b262a 100644 --- a/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html +++ b/latest/generated/sgkit.variables.stat_Garud_h2_h1_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html index a8faba57a..27d71fa03 100644 --- a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html +++ b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html index 34b9aa0f4..301d17102 100644 --- a/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html +++ b/latest/generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html b/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html index 61d6e69f3..be8ebe673 100644 --- a/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html +++ b/latest/generated/sgkit.variables.stat_Tajimas_D_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_Tajimas_D_spec#

    -sgkit.variables.stat_Tajimas_D_spec = ArrayLikeSpec(default_name='stat_Tajimas_D', __doc__='Tajima’s D for cohorts.', kind='f', ndim=2, dims=({'variants', 'windows'}, 'cohorts'))#
    +sgkit.variables.stat_Tajimas_D_spec = ArrayLikeSpec(default_name='stat_Tajimas_D', __doc__='Tajima’s D for cohorts.', kind='f', ndim=2, dims=({'windows', 'variants'}, 'cohorts'))#

    Tajima’s D for cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html b/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html index 5b4b2e442..0165cac01 100644 --- a/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html +++ b/latest/generated/sgkit.variables.stat_Weir_Goudet_beta_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_Weir_Goudet_beta_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.stat_Weir_Goudet_beta_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_divergence_spec.html b/latest/generated/sgkit.variables.stat_divergence_spec.html index 58955148e..bef72d007 100644 --- a/latest/generated/sgkit.variables.stat_divergence_spec.html +++ b/latest/generated/sgkit.variables.stat_divergence_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_divergence_spec#

    -sgkit.variables.stat_divergence_spec = ArrayLikeSpec(default_name='stat_divergence', __doc__='Genetic divergence between pairs of cohorts.', kind='f', ndim=3, dims=({'variants', 'windows'}, 'cohorts_0', 'cohorts_1'))#
    +sgkit.variables.stat_divergence_spec = ArrayLikeSpec(default_name='stat_divergence', __doc__='Genetic divergence between pairs of cohorts.', kind='f', ndim=3, dims=({'windows', 'variants'}, 'cohorts_0', 'cohorts_1'))#

    Genetic divergence between pairs of cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_diversity_spec.html b/latest/generated/sgkit.variables.stat_diversity_spec.html index af0b6f8c6..763ad54aa 100644 --- a/latest/generated/sgkit.variables.stat_diversity_spec.html +++ b/latest/generated/sgkit.variables.stat_diversity_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_diversity_spec#

    -sgkit.variables.stat_diversity_spec = ArrayLikeSpec(default_name='stat_diversity', __doc__='Genetic diversity (also known as "Tajima’s pi") for cohorts.', kind='f', ndim=2, dims=({'variants', 'windows'}, 'cohorts'))#
    +sgkit.variables.stat_diversity_spec = ArrayLikeSpec(default_name='stat_diversity', __doc__='Genetic diversity (also known as "Tajima’s pi") for cohorts.', kind='f', ndim=2, dims=({'windows', 'variants'}, 'cohorts'))#

    Genetic diversity (also known as “Tajima’s pi”) for cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html b/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html index 36d7f69e0..8eb286ab6 100644 --- a/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html +++ b/latest/generated/sgkit.variables.stat_genomic_kinship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_genomic_kinship_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.stat_genomic_kinship_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html b/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html index 7e7e4bfcb..1e38c3644 100644 --- a/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_genomic_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html b/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html index 6c89d1217..0f1bf45c2 100644 --- a/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html b/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html index 2a161794b..982acdf19 100644 --- a/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_hybrid_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_identity_by_state_spec.html b/latest/generated/sgkit.variables.stat_identity_by_state_spec.html index a9d3d118a..f6250f8f0 100644 --- a/latest/generated/sgkit.variables.stat_identity_by_state_spec.html +++ b/latest/generated/sgkit.variables.stat_identity_by_state_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html b/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html index 0033d35eb..dee870a48 100644 --- a/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_inverse_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html b/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html index 8a7642813..e2818d47b 100644 --- a/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html +++ b/latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_observed_heterozygosity_spec#

    -sgkit.variables.stat_observed_heterozygosity_spec = ArrayLikeSpec(default_name='stat_observed_heterozygosity', __doc__='\nObserved heterozygosity for cohorts.\n', kind='f', ndim=2, dims=({'variants', 'windows'}, 'cohorts'))#
    +sgkit.variables.stat_observed_heterozygosity_spec = ArrayLikeSpec(default_name='stat_observed_heterozygosity', __doc__='\nObserved heterozygosity for cohorts.\n', kind='f', ndim=2, dims=({'windows', 'variants'}, 'cohorts'))#

    Observed heterozygosity for cohorts.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_pbs_spec.html b/latest/generated/sgkit.variables.stat_pbs_spec.html index 2a4d4a865..af0c54014 100644 --- a/latest/generated/sgkit.variables.stat_pbs_spec.html +++ b/latest/generated/sgkit.variables.stat_pbs_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.stat_pbs_spec#

    -sgkit.variables.stat_pbs_spec = ArrayLikeSpec(default_name='stat_pbs', __doc__='Population branching statistic for cohort triples.', kind='f', ndim=4, dims=({'variants', 'windows'}, 'cohorts_0', 'cohorts_1', 'cohorts_2'))#
    +sgkit.variables.stat_pbs_spec = ArrayLikeSpec(default_name='stat_pbs', __doc__='Population branching statistic for cohort triples.', kind='f', ndim=4, dims=({'windows', 'variants'}, 'cohorts_0', 'cohorts_1', 'cohorts_2'))#

    Population branching statistic for cohort triples.

    - - +
    diff --git a/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html b/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html index f8efabd49..9c71e9a7f 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_contribution_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.stat_pedigree_contribution_spec#

    @@ -758,8 +753,7 @@

    sgkit.variables.stat_pedigree_contribution_spec - - +

    diff --git a/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html b/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html index 6a05e846d..fdf8a824a 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_inbreeding_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html index 3c232edde..519a10b92 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html index f0dc86ef3..9c9df7735 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html index be71e1e46..78b7941d0 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_kinship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html b/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html index 2fdfdae8b..555cb08e5 100644 --- a/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html +++ b/latest/generated/sgkit.variables.stat_pedigree_relationship_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.traits_spec.html b/latest/generated/sgkit.variables.traits_spec.html index 580adf33f..bf72183a8 100644 --- a/latest/generated/sgkit.variables.traits_spec.html +++ b/latest/generated/sgkit.variables.traits_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_count_spec.html b/latest/generated/sgkit.variables.variant_allele_count_spec.html index 0968a654b..128debcda 100644 --- a/latest/generated/sgkit.variables.variant_allele_count_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_frequency_spec.html b/latest/generated/sgkit.variables.variant_allele_frequency_spec.html index 06de2870b..86b7592e6 100644 --- a/latest/generated/sgkit.variables.variant_allele_frequency_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_frequency_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_spec.html b/latest/generated/sgkit.variables.variant_allele_spec.html index c5fbdfc91..1d455d29a 100644 --- a/latest/generated/sgkit.variables.variant_allele_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_allele_total_spec.html b/latest/generated/sgkit.variables.variant_allele_total_spec.html index cc2ac0676..6fa798209 100644 --- a/latest/generated/sgkit.variables.variant_allele_total_spec.html +++ b/latest/generated/sgkit.variables.variant_allele_total_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_call_rate_spec.html b/latest/generated/sgkit.variables.variant_call_rate_spec.html index abe49dbf6..646d058e0 100644 --- a/latest/generated/sgkit.variables.variant_call_rate_spec.html +++ b/latest/generated/sgkit.variables.variant_call_rate_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_contig_spec.html b/latest/generated/sgkit.variables.variant_contig_spec.html index a768ee167..3889fc033 100644 --- a/latest/generated/sgkit.variables.variant_contig_spec.html +++ b/latest/generated/sgkit.variables.variant_contig_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.variant_contig_spec#

    -sgkit.variables.variant_contig_spec = ArrayLikeSpec(default_name='variant_contig', __doc__='\nIndex corresponding to contig name for each variant. In some less common\nscenarios, this may also be equivalent to the contig names if the data\ngenerating process used contig names that were also integers.\n', kind={'i', 'u'}, ndim=1, dims=('variants',))#
    +sgkit.variables.variant_contig_spec = ArrayLikeSpec(default_name='variant_contig', __doc__='\nIndex corresponding to contig name for each variant. In some less common\nscenarios, this may also be equivalent to the contig names if the data\ngenerating process used contig names that were also integers.\n', kind={'u', 'i'}, ndim=1, dims=('variants',))#

    Index corresponding to contig name for each variant. In some less common scenarios, this may also be equivalent to the contig names if the data generating process used contig names that were also integers.

    @@ -757,8 +752,7 @@

    sgkit.variables.variant_contig_spec - - +

    diff --git a/latest/generated/sgkit.variables.variant_genotype_count_spec.html b/latest/generated/sgkit.variables.variant_genotype_count_spec.html index dff3aa806..59e939cb9 100644 --- a/latest/generated/sgkit.variables.variant_genotype_count_spec.html +++ b/latest/generated/sgkit.variables.variant_genotype_count_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,12 +739,11 @@
    - -
    +

    sgkit.variables.variant_genotype_count_spec#

    -sgkit.variables.variant_genotype_count_spec = ArrayLikeSpec(default_name='variant_genotype_count', __doc__='\nThe number of observations for each possible genotype at each variant.\nCounts are sorted following the ordering defined in the VCF specification.\n\n- For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``\n  (homozygous reference, heterozygous, homozygous alternate).\n- For triallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``,\n  ``02``, ``12``, ``22``\n- For triallelic, triploid genotypes the ordering is  ``000``, ``001``, ``011``,\n  ``111``, ``002``, ``012``, ``112``, ``022``, ``122``, ``222``\n', kind={'i', 'u'}, ndim=2, dims=('variants', 'genotypes'))#
    +sgkit.variables.variant_genotype_count_spec = ArrayLikeSpec(default_name='variant_genotype_count', __doc__='\nThe number of observations for each possible genotype at each variant.\nCounts are sorted following the ordering defined in the VCF specification.\n\n- For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``\n  (homozygous reference, heterozygous, homozygous alternate).\n- For triallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``,\n  ``02``, ``12``, ``22``\n- For triallelic, triploid genotypes the ordering is  ``000``, ``001``, ``011``,\n  ``111``, ``002``, ``012``, ``112``, ``022``, ``122``, ``222``\n', kind={'u', 'i'}, ndim=2, dims=('variants', 'genotypes'))#

    The number of observations for each possible genotype at each variant. Counts are sorted following the ordering defined in the VCF specification.

      @@ -764,8 +759,7 @@

      sgkit.variables.variant_genotype_count_spec - - +

    diff --git a/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html b/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html index 0a78abefd..c9586a3ec 100644 --- a/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html +++ b/latest/generated/sgkit.variables.variant_hwe_p_value_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_id_spec.html b/latest/generated/sgkit.variables.variant_id_spec.html index ffe976cfe..17963f0eb 100644 --- a/latest/generated/sgkit.variables.variant_id_spec.html +++ b/latest/generated/sgkit.variables.variant_id_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,20 +739,18 @@
    - -
    +

    sgkit.variables.variant_id_spec#

    -sgkit.variables.variant_id_spec = ArrayLikeSpec(default_name='variant_id', __doc__='The unique identifier of the variant.', kind={'U', 'S', 'O'}, ndim=1, dims=('variants',))#
    +sgkit.variables.variant_id_spec = ArrayLikeSpec(default_name='variant_id', __doc__='The unique identifier of the variant.', kind={'S', 'U', 'O'}, ndim=1, dims=('variants',))#

    The unique identifier of the variant.

    - - +
    diff --git a/latest/generated/sgkit.variables.variant_linreg_beta_spec.html b/latest/generated/sgkit.variables.variant_linreg_beta_spec.html index 2a2415f19..a87ee01d0 100644 --- a/latest/generated/sgkit.variables.variant_linreg_beta_spec.html +++ b/latest/generated/sgkit.variables.variant_linreg_beta_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@
    - -
    +

    sgkit.variables.variant_linreg_beta_spec#

    @@ -755,8 +750,7 @@

    sgkit.variables.variant_linreg_beta_spec - - +

    diff --git a/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html b/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html index 622408ffd..15f36ab4b 100644 --- a/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html +++ b/latest/generated/sgkit.variables.variant_linreg_p_value_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html b/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html index 7116a0b62..142e94bda 100644 --- a/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html +++ b/latest/generated/sgkit.variables.variant_linreg_t_value_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_called_spec.html b/latest/generated/sgkit.variables.variant_n_called_spec.html index 0fd95122f..659a1aeef 100644 --- a/latest/generated/sgkit.variables.variant_n_called_spec.html +++ b/latest/generated/sgkit.variables.variant_n_called_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_het_spec.html b/latest/generated/sgkit.variables.variant_n_het_spec.html index de052a7f3..b48cc516f 100644 --- a/latest/generated/sgkit.variables.variant_n_het_spec.html +++ b/latest/generated/sgkit.variables.variant_n_het_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html b/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html index 8acd2a98f..1e9d24506 100644 --- a/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html +++ b/latest/generated/sgkit.variables.variant_n_hom_alt_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html b/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html index dda31c706..da45db9c5 100644 --- a/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html +++ b/latest/generated/sgkit.variables.variant_n_hom_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_n_non_ref_spec.html b/latest/generated/sgkit.variables.variant_n_non_ref_spec.html index 1c01012a0..dfd28813c 100644 --- a/latest/generated/sgkit.variables.variant_n_non_ref_spec.html +++ b/latest/generated/sgkit.variables.variant_n_non_ref_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_ploidy_spec.html b/latest/generated/sgkit.variables.variant_ploidy_spec.html index c9b470b5a..734f64de2 100644 --- a/latest/generated/sgkit.variables.variant_ploidy_spec.html +++ b/latest/generated/sgkit.variables.variant_ploidy_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_position_spec.html b/latest/generated/sgkit.variables.variant_position_spec.html index 4136ad84e..d5b6df37f 100644 --- a/latest/generated/sgkit.variables.variant_position_spec.html +++ b/latest/generated/sgkit.variables.variant_position_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.variant_score_spec.html b/latest/generated/sgkit.variables.variant_score_spec.html index 4078f4f16..15b49029f 100644 --- a/latest/generated/sgkit.variables.variant_score_spec.html +++ b/latest/generated/sgkit.variables.variant_score_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.window_contig_spec.html b/latest/generated/sgkit.variables.window_contig_spec.html index 8deb83234..04b12fe3b 100644 --- a/latest/generated/sgkit.variables.window_contig_spec.html +++ b/latest/generated/sgkit.variables.window_contig_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.window_start_spec.html b/latest/generated/sgkit.variables.window_start_spec.html index 9d0ad828e..67a3dba1b 100644 --- a/latest/generated/sgkit.variables.window_start_spec.html +++ b/latest/generated/sgkit.variables.window_start_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variables.window_stop_spec.html b/latest/generated/sgkit.variables.window_stop_spec.html index f9557fb4b..ef11b4978 100644 --- a/latest/generated/sgkit.variables.window_stop_spec.html +++ b/latest/generated/sgkit.variables.window_stop_spec.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.variant_stats.html b/latest/generated/sgkit.variant_stats.html index ff6cdc443..4a3445485 100644 --- a/latest/generated/sgkit.variant_stats.html +++ b/latest/generated/sgkit.variant_stats.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_genome.html b/latest/generated/sgkit.window_by_genome.html index 2f7b71cc7..aef92e860 100644 --- a/latest/generated/sgkit.window_by_genome.html +++ b/latest/generated/sgkit.window_by_genome.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_interval.html b/latest/generated/sgkit.window_by_interval.html index 947ac65ea..6eb45a1ec 100644 --- a/latest/generated/sgkit.window_by_interval.html +++ b/latest/generated/sgkit.window_by_interval.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_position.html b/latest/generated/sgkit.window_by_position.html index 2645b9fdc..9c91737d8 100644 --- a/latest/generated/sgkit.window_by_position.html +++ b/latest/generated/sgkit.window_by_position.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/generated/sgkit.window_by_variant.html b/latest/generated/sgkit.window_by_variant.html index b4467e78b..fed960c11 100644 --- a/latest/generated/sgkit.window_by_variant.html +++ b/latest/generated/sgkit.window_by_variant.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -743,8 +739,7 @@ diff --git a/latest/getting_started.html b/latest/getting_started.html index 12fc4aaaf..6560deea4 100644 --- a/latest/getting_started.html +++ b/latest/getting_started.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@ diff --git a/latest/how_do_i.html b/latest/how_do_i.html index 9daa63deb..f16cca307 100644 --- a/latest/how_do_i.html +++ b/latest/how_do_i.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@ diff --git a/latest/index.html b/latest/index.html index d925c2e48..5128e56f8 100644 --- a/latest/index.html +++ b/latest/index.html @@ -55,13 +55,9 @@ - - + - - - - + @@ -515,8 +511,7 @@ diff --git a/latest/news.html b/latest/news.html index 02f8c6537..180a233a3 100644 --- a/latest/news.html +++ b/latest/news.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@ diff --git a/latest/news/introducing_sgkit.html b/latest/news/introducing_sgkit.html index ec506681c..cbe66b77a 100644 --- a/latest/news/introducing_sgkit.html +++ b/latest/news/introducing_sgkit.html @@ -54,13 +54,9 @@ - - + - - - - + @@ -540,8 +536,7 @@
    - -
    +

    Introducing sgkit#

    The sgkit team is pleased to announce the release of sgkit 0.5.0! This release adds support for the VCF Zarr specification, which describes an encoding of VCF data in chunked-columnar form using the Zarr format.

    With this release, we also introduce our news page, where we will announce future releases and provide other relevant updates for the sgkit project.

    @@ -551,10 +546,7 @@

    Introducing sgkit - - - - +
    @@ -564,8 +556,6 @@

    Introducing sgkit - - + - - - - + diff --git a/latest/searchindex.js b/latest/searchindex.js index f6749e492..4460b9a82 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, 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, 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, 4, 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, 4, 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, 4, 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, 4, 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, 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, "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, "tomwhit": 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, "tutori": [2, 168], "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, 4, 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, 4, 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, 4, 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, 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, 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, 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, 4, 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, 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, 4, 46, 47, 65, 173], "about": [3, 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, 4, 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, 4, 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, 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, 4, 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, 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, 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, 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, 4, 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], "updat": [3, 6, 172, 173], "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, 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, "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, 6, 36, 38, 51, 52, 56, 168, 173], "command": [3, 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, 4, 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, 4, 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], "next": [4, 6], "filesystem": [4, 174], "max_alt_allel": [4, 45, 46, 47], "gt": [4, 6, 173], "dp": [4, 45, 46, 47], "gq": 4, "field_def": [4, 45, 46, 47, 65, 174], "tmp": [4, 6, 174], "ipykernel_2670": 4, "2446290678": 4, "deprecationwarn": 4, "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], "argument": [4, 17, 23, 29, 53, 56, 68, 168, 173, 174], "load": [4, 6, 37, 39, 40, 45, 46, 48, 53, 65, 111, 168, 170, 173, 174], "extra": [4, 36, 38, 45, 46, 47, 65, 173, 174], "interest": [4, 70], "definit": [4, 45, 46, 47, 65, 170], "unknown": [4, 6, 25, 28, 29, 57, 60, 61, 62, 63, 69, 95, 120, 168, 169, 173], "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], "65mb": 4, "10879": 4, "284": [4, 26], "84": 4, "coordin": [4, 6, 18, 27, 64, 66, 164, 166, 167, 168, 169, 173, 174], "12": [4, 6, 56, 146, 166, 168, 169, 173, 174], "17": [4, 62, 168, 169, 173], "call_ad": 4, "int32": [4, 174], "25mb": 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, "12mb": 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], "int8": [4, 168, 169, 173, 174], "6mb": 4, "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], "3mb": 4, "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], "44kb": 4, "variant_qu": 4, "float32": [4, 37], "7": [4, 6, 10, 13, 36, 38, 45, 46, 47, 56, 62, 63, 167, 168, 169, 170, 173, 174], "datasetdimens": [4, 6], "10879sampl": 4, "284allel": 4, "2ploidi": 4, "2contig": 4, "84filter": 4, "1coordin": 4, "int32dask": 4, "byte": [4, 6, 36, 37, 38, 39, 42, 43, 44, 45, 46, 49, 50, 53, 68, 174], "23": [4, 56, 168, 169, 173, 174], "57": [4, 168], "mib": [4, 6], "21": [4, 6, 56, 166, 168, 169, 173, 174], "67": [4, 6, 168], "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], "11": [4, 6, 25, 56, 146, 168, 169, 173], "79": 4, "10": [4, 6, 10, 13, 19, 45, 46, 47, 52, 56, 66, 164, 166, 167, 168, 169, 170, 173, 174], "83": 4, "int8dask": 4, "second": [4, 24, 26, 30, 46, 64, 84, 89, 139, 168, 174], "mixed_ploidi": [4, 45, 46, 47, 168, 174], "89": 4, "42": [4, 168, 173], "booldask": 4, "flag": [4, 26, 73, 75, 77, 78, 80, 81, 82, 168], "unphas": [4, 19, 70, 81], "95": [4, 168], "71": [4, 28, 29], "u10dask": 4, "28": [4, 168, 173], "kib": 4, "u10": 4, "int64dask": 4, "672": 4, "b": [4, 6, 25, 73, 75, 77, 78, 80, 81, 82, 168, 169, 173], "int64": [4, 164, 166, 167, 168, 169, 173], "objectdask": 4, "8": [4, 6, 10, 13, 59, 166, 167, 168, 169, 170, 173, 174], "sample_id": [4, 6, 40, 41, 57, 60, 61, 62, 63, 64, 69, 102, 168, 169, 174], "uniqu": [4, 6, 61, 62, 63, 79, 94, 102, 148, 173], "22": [4, 6, 56, 146, 168, 169, 173, 174], "variant_allel": [4, 45, 46, 47, 69, 142, 168, 169, 173, 174], "169": 4, "98": [4, 59, 168], "156": 4, "25": [4, 8, 10, 12, 28, 29, 35, 60, 61, 63, 166, 168, 173], "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], "scenario": [4, 145], "equival": [4, 29, 44, 108, 110, 145, 169], "process": [4, 6, 45, 46, 47, 48, 49, 54, 119, 145, 169, 170, 173, 174], "62": [4, 168], "77": 4, "99": [4, 168, 169], "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], "06": [4, 24, 66], "float32dask": 4, "249250621": 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, "16569": 4, "4262": 4, "15008": 4, "19913": 4, "27386": 4, "27682": 4, "33824": 4, "34474": 4, "36148": 4, "36422": 4, "36651": 4, "37175": 4, "37498": 4, "38154": 4, "38502": 4, "38914": 4, "39786": 4, "39929": 4, "39939": 4, "40103": 4, "40531": 4, "40652": 4, "41001": 4, "41933": 4, "41934": 4, "42152": 4, "43341": 4, "43523": 4, "43691": 4, "45867": 4, "45941": 4, "81310": 4, "90085": 4, "92689": 4, "106433": 4, "128374": 4, "129120": 4, "137718": 4, "155397": 4, "159169": 4, "161147": 4, "161802": 4, "164239": 4, "166566": 4, "169874": 4, "172149": 4, "172294": 4, "172545": 4, "174588": 4, "179198": 4, "179693": 4, "180455": 4, "182896": 4, "186858": 4, "186861": 4, "187035": 4, "189789": 4, "191469": 4, "211173": 4, "547496": 4, "x27": [4, 6], "6": [4, 6, 10, 13, 24, 25, 52, 56, 58, 62, 63, 166, 167, 168, 169, 170, 173, 174], "13": [4, 56, 168, 169, 173], "14": [4, 56, 168, 169, 173], "15": [4, 168, 169, 173], "18": [4, 59, 168, 169, 173], "19": [4, 13, 66, 168, 169, 173], "20": [4, 13, 38, 56, 168, 169, 173, 174], "mt": 4, "gl000207": 4, "gl000226": 4, "gl000229": 4, "gl000231": 4, "gl000210": 4, "gl000239": 4, "gl000235": 4, "gl000201": 4, "gl000247": 4, "gl000245": 4, "gl000197": 4, "gl000203": 4, "gl000246": 4, "gl000249": 4, "gl000196": 4, "gl000248": 4, "gl000244": 4, "gl000238": 4, "gl000202": 4, "gl000234": 4, "gl000232": 4, "gl000206": 4, "gl000240": 4, "gl000236": 4, "gl000241": 4, "gl000243": 4, "gl000242": 4, "gl000230": 4, "gl000237": 4, "gl000233": 4, "gl000204": 4, "gl000198": 4, "gl000208": 4, "gl000191": 4, "gl000227": 4, "gl000228": 4, "gl000214": 4, "gl000221": 4, "gl000209": 4, "gl000218": 4, "gl000220": 4, "gl000213": 4, "gl000211": 4, "gl000199": 4, "gl000217": 4, "gl000216": 4, "gl000215": 4, "gl000205": 4, "gl000219": 4, "gl000224": 4, "gl000223": 4, "gl000195": 4, "gl000212": 4, "gl000222": 4, "gl000200": 4, "gl000193": 4, "gl000194": 4, "gl000225": 4, "gl000192": 4, "max_alt_alleles_seen": [4, 174], "1sourc": 4, "unknownvcf_head": 4, "fileformat": 4, "vcfv4": [4, 45, 46, 47, 65], "id": [4, 6, 8, 18, 58], "descript": [4, 45, 46, 47, 65, 66], "quot": 4, "hailvers": 4, "29fbaeaf265": 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, "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], "assembli": 4, "grch37": 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], "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, "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, "drop": [4, 6, 45, 46, 47, 54, 64, 69, 93, 169], "66mb": 4, "435kb": 4, "2kb": [4, 66, 168, 169, 173], "284b": 4, "284variant": 4, "10879allel": 4, "424": 4, "96": [4, 168], "390": 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], "float64": [4, 6, 66, 168, 169], "fewer": [4, 45, 46, 47, 61, 62, 63, 168, 174], "len": 4, "76": [4, 27], "72": 4, "55": [4, 63, 166, 168], "47": [4, 26, 168, 173], "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, "poor": 4, "iter": 4, "collect": 4, "metric": [4, 56], "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], "float64dask": 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], "70": 4, "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], "59mb": 4, "38": [4, 168, 173], "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, "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], "07": 4, "54": [4, 168], "59": [4, 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], "00": [4, 56, 146, 173], "01": [4, 6, 28, 56, 59, 146, 171], "triallel": [4, 146], "02": [4, 56, 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], "36": [4, 168, 173], "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], "63mb": 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], "58": [4, 168], "49": [4, 168, 173], "33": [4, 56, 168, 173], "196": 4, "73": [4, 28, 29], "127": [4, 59], "48": [4, 59, 168, 173, 174], "131": [4, 61, 62, 63, 69], "37": [4, 168, 173], "31": [4, 56, 168, 173], "32": [4, 13, 56, 69, 168, 173, 174], "327": 4, "212": 4, "46": [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, "26": [4, 168, 173], "128805": 4, "008168": 4, "8012085": 4, "24": [4, 56, 168, 170, 173], "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, "28mb": [4, 6], "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, "40": [4, 166, 168, 173], "int16dask": 4, "66": [4, 168], "27": [4, 63, 168, 173], "81": 4, "82": 4, "29": [4, 168, 173], "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, "twice": 6, "unfortun": 6, "propag": [6, 61, 62, 63], "assign_coord": [6, 18, 58, 64, 168], "lazi": [6, 168], "think": [6, 172], "promis": 6, "point": [6, 173], "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], "ipykernel_2721": 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], "specifi": [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], "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], "05": [13, 25], "call_genotype_index": [13, 79, 173], "35": [13, 63, 168, 173], "44": [13, 168, 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], "liter": [17, 25, 28, 29, 30, 56, 60, 61, 62, 63, 69], "multiset": 18, "cardin": 18, "document": [18, 168, 169, 170, 173, 174], "manner": 19, "denot": [19, 56], "separ": [19, 46, 66, 139, 168, 173, 174], "genotype_phas": 19, "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], "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, "applic": [25, 27, 36, 38, 41, 59, 70, 174], "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], "90": 26, "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, "93": [27, 28, 29], "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], "92": [28, 29], "4656": [28, 29], "4663": [28, 29], "johnson": [28, 29], "tsuruta": [28, 29], "lawlor": [28, 29], "holstein": [28, 29], "score": [28, 29, 112, 159], "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], "temporari": [36, 38, 45, 46, 174], "intermedi": [36, 38, 45, 46, 62, 173, 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], "tbi": [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], "truncate_cal": [45, 46, 47, 174], "exclude_field": [45, 46, 47], "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], "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], "03": 56, "04": [56, 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, "third": [61, 62, 63, 64, 168, 172], "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], "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], "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, "51": [168, 173], "53": 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, "56": 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, "forc": 168, "client": [168, 173, 174], "coerc": 168, "asarrai": 168, "63": 168, "22kb": [168, 173], "600b": [168, 169], "68": 168, "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, "1kb": 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, "08": 171, "team": [171, 172], "announc": [171, 172], "columnar": [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, "scan": 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, "bash": 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, "181": 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}, "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, "9": 2, "24": 2, "june": 2, "2024": 2, "deprec": 2, "improv": 2, "8": 2, "1": 2, "mai": 2, "bug": 2, "fix": 2, "document": [2, 3], "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, "id3"], [2, "id7"]], "0.9.0 (24 June 2024)": [[2, "june-2024"]], "Deprecations": [[2, "deprecations"], [2, "id4"]], "Improvements": [[2, "improvements"], [2, "id2"], [2, "id5"], [2, "id9"]], "0.8.0 (1 May 2024)": [[2, "may-2024"]], "Bug fixes": [[2, "bug-fixes"], [2, "id6"], [2, "id10"]], "Documentation": [[2, "documentation"]], "0.7.0 (2 May 2023)": [[2, "may-2023"]], "Breaking changes": [[2, "breaking-changes"], [2, "id8"]], "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, 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 diff --git a/latest/user_guide.html b/latest/user_guide.html index 1a177266e..41df0842b 100644 --- a/latest/user_guide.html +++ b/latest/user_guide.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@ diff --git a/latest/vcf.html b/latest/vcf.html index d17e04e1e..7a88bcdc3 100644 --- a/latest/vcf.html +++ b/latest/vcf.html @@ -56,13 +56,9 @@ - - + - - - - + @@ -549,8 +545,7 @@