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BimberLab · Aug 2, 2023 · 4524f26 · 4524f26
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diff --git a/toolDoc/com_github_discvrseq_walkers_AnnotateNovelSites.html b/toolDoc/com_github_discvrseq_walkers_AnnotateNovelSites.html
@@ -1209,7 +1209,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_AppendGenotypes.html b/toolDoc/com_github_discvrseq_walkers_AppendGenotypes.html
@@ -990,7 +990,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_BackportLiftedVcf.html b/toolDoc/com_github_discvrseq_walkers_BackportLiftedVcf.html
@@ -1001,7 +1001,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_ClinvarAnnotator.html b/toolDoc/com_github_discvrseq_walkers_ClinvarAnnotator.html
@@ -1000,7 +1000,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_ClipOverlappingAlignments.html b/toolDoc/com_github_discvrseq_walkers_ClipOverlappingAlignments.html
@@ -1005,7 +1005,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_CrossSampleGenotypeComparison.html b/toolDoc/com_github_discvrseq_walkers_CrossSampleGenotypeComparison.html
@@ -1054,7 +1054,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_ExtendedFuncotator.html b/toolDoc/com_github_discvrseq_walkers_ExtendedFuncotator.html
@@ -1350,7 +1350,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_FindGenomeDifferences.html b/toolDoc/com_github_discvrseq_walkers_FindGenomeDifferences.html
@@ -1065,7 +1065,7 @@ <h3><a name="--windowSize">--windowSize </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_GenotypeFilterBySample.html b/toolDoc/com_github_discvrseq_walkers_GenotypeFilterBySample.html
@@ -1007,7 +1007,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_GroupCompare.html b/toolDoc/com_github_discvrseq_walkers_GroupCompare.html
@@ -1240,7 +1240,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_ImmunoGenotyper.html b/toolDoc/com_github_discvrseq_walkers_ImmunoGenotyper.html
@@ -1180,7 +1180,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_MergeFastqReads.html b/toolDoc/com_github_discvrseq_walkers_MergeFastqReads.html
@@ -1062,7 +1062,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_MergeVariantSites.html b/toolDoc/com_github_discvrseq_walkers_MergeVariantSites.html
@@ -1093,7 +1093,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_MergeVcfsAndGenotypes.html b/toolDoc/com_github_discvrseq_walkers_MergeVcfsAndGenotypes.html
@@ -1392,7 +1392,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_MultiSourceAnnotator.html b/toolDoc/com_github_discvrseq_walkers_MultiSourceAnnotator.html
@@ -1159,7 +1159,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_MultipleAllelesAtLoci.html b/toolDoc/com_github_discvrseq_walkers_MultipleAllelesAtLoci.html
@@ -1084,7 +1084,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_OutputVariantsStartingInIntervals.html b/toolDoc/com_github_discvrseq_walkers_OutputVariantsStartingInIntervals.html
@@ -978,7 +978,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_PrintReadBackedHaplotypes.html b/toolDoc/com_github_discvrseq_walkers_PrintReadBackedHaplotypes.html
@@ -1080,7 +1080,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_PrintReadsContaining.html b/toolDoc/com_github_discvrseq_walkers_PrintReadsContaining.html
@@ -1247,7 +1247,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_RemoveAnnotations.html b/toolDoc/com_github_discvrseq_walkers_RemoveAnnotations.html
@@ -1158,7 +1158,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_SampleSpecificGenotypeFiltration.html b/toolDoc/com_github_discvrseq_walkers_SampleSpecificGenotypeFiltration.html
@@ -1086,7 +1086,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_SplitVcfBySamples.html b/toolDoc/com_github_discvrseq_walkers_SplitVcfBySamples.html
@@ -1057,7 +1057,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_Summarize10xAlignments.html b/toolDoc/com_github_discvrseq_walkers_Summarize10xAlignments.html
@@ -957,7 +957,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_VariantConcordanceScore.html b/toolDoc/com_github_discvrseq_walkers_VariantConcordanceScore.html
@@ -1102,7 +1102,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_VcfComparison.html b/toolDoc/com_github_discvrseq_walkers_VcfComparison.html
@@ -1183,7 +1183,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_VcfFilterComparison.html b/toolDoc/com_github_discvrseq_walkers_VcfFilterComparison.html
@@ -1062,7 +1062,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_VcfToLuceneIndexer.html b/toolDoc/com_github_discvrseq_walkers_VcfToLuceneIndexer.html
@@ -176,6 +176,13 @@ <h3>VcfToLuceneIndexer specific arguments</h3>
 					<td>false</td>
 					<td>display the help message</td>
 				</tr>
+				<tr>
+					<td><a href="#--index-stats">--index-stats</a><br />
+					</td>
+					<!--<td>GATKPath</td> -->
+					<td>null</td>
+					<td>A file where a TSV of summary information about each indexed field will be written, including min/max value and a list of unique values</td>
+				</tr>
 				<tr>
 					<td><a href="#--info-field">--info-field</a><br />
 								&nbsp;<em>-IF</em>
@@ -204,7 +211,7 @@ <h3>VcfToLuceneIndexer specific arguments</h3>
 					<td><a href="#--output">--output</a><br />
 								&nbsp;<em>-O</em>
 					</td>
-					<!--<td>File</td> -->
+					<!--<td>GATKPath</td> -->
 					<td>null</td>
 					<td>Output file (if not provided, defaults to STDOUT)</td>
 				</tr>
@@ -811,6 +818,18 @@ <h3><a name="--help">--help </a>
 			&nbsp;<span class="label">false</span>
 		</p>
 		<hr style="border-bottom: dotted 1px #C0C0C0;" />
+		<h3><a name="--index-stats">--index-stats </a>
+			 / <small>NA</small>
+		</h3>
+		<p class="args">
+			<b>A file where a TSV of summary information about each indexed field will be written, including min/max value and a list of unique values</b><br />
+
+		</p>
+		<p>
+		<span class="label label-info ">GATKPath</span>
+			&nbsp;<span class="label">null</span>
+		</p>
+		<hr style="border-bottom: dotted 1px #C0C0C0;" />
 		<h3><a name="--info-field">--info-field </a>
 			 / <small>-IF</small>
 		</h3>
@@ -963,7 +982,7 @@ <h3><a name="--output">--output </a>
 
 		</p>
 		<p>
-		<span class="label label-info ">File</span>
+		<span class="label label-info ">GATKPath</span>
 			&nbsp;<span class="label">null</span>
 		</p>
 		<hr style="border-bottom: dotted 1px #C0C0C0;" />
@@ -1232,7 +1251,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_VcfToLuceneIndexer.json b/toolDoc/com_github_discvrseq_walkers_VcfToLuceneIndexer.json
@@ -417,6 +417,22 @@
       "deprecated": false,
       "options": []
     },
+    {
+      "summary": "A file where a TSV of summary information about each indexed field will be written, including min/max value and a list of unique values",
+      "name": "--index-stats",
+      "synonyms": "NA",
+      "type": "GATKPath",
+      "required": "no",
+      "fulltext": "",
+      "defaultValue": "null",
+      "minValue": "NA",
+      "maxValue": "NA",
+      "minRecValue": "NA",
+      "maxRecValue": "NA",
+      "kind": "optional",
+      "deprecated": false,
+      "options": []
+    },
     {
       "summary": "Info fields to index",
       "name": "--info-field",
@@ -583,7 +599,7 @@
       "summary": "Output file (if not provided, defaults to STDOUT)",
       "name": "--output",
       "synonyms": "-O",
-      "type": "File",
+      "type": "GATKPath",
       "required": "no",
       "fulltext": "",
       "defaultValue": "null",

diff --git a/toolDoc/com_github_discvrseq_walkers_annotator_DiscvrVariantAnnotator.html b/toolDoc/com_github_discvrseq_walkers_annotator_DiscvrVariantAnnotator.html
@@ -1305,7 +1305,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_tagpcr_IntegrationSiteMapper.html b/toolDoc/com_github_discvrseq_walkers_tagpcr_IntegrationSiteMapper.html
@@ -1482,7 +1482,7 @@ <h3><a name="--write-default-descriptors">--write-default-descriptors </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/com_github_discvrseq_walkers_variantqc_VariantQC.html b/toolDoc/com_github_discvrseq_walkers_variantqc_VariantQC.html
@@ -1304,7 +1304,7 @@ <h3><a name="--version">--version </a>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>
diff --git a/toolDoc/index.html b/toolDoc/index.html
@@ -13,7 +13,7 @@ <h1 id="top"><i class='<?php print ico::toolDocsIcon; ?>'></i>DISCVR-Seq Toolkit
             <div class="span6">
                 <div class="btn-group pull-right">
                     <a class="btn btn-warning dropdown-toggle" data-toggle="dropdown" href="#">
-                        Version 1.3.47
+                        Version 1.3.48
                         <span class="caret"></span>
                     </a>
                 </div>
@@ -230,7 +230,7 @@ <h4>Variant Manipulation</h4>
         	<a href="https://github.com/bimberlab/discvrseq/issues/">Issues/Help</a>
         </p>
 
-        <p class="version">DISCVR-Seq version 1.3.47 built at 22-07-2023 02:24:05.
+        <p class="version">DISCVR-Seq version 1.3.48 built at 02-08-2023 02:14:28.
         </p>
 
 </div></div>