Conditionalize GenotypeGVCFs and ExcessHet/InbreedingCoef

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantProcessingPanel.js

@@ -268,6 +268,12 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 				label: 'Intervals to Exclude',
 				description: 'A BED or similar file with intervals to skip',
 				defaultValue: null
+			},{
+				fieldXtype: 'ldk-expdatafield',
+				name: 'skipExcessHetAndInbreeding',
+				label: 'Skip Excess Het And Inbreeding',
+				description: 'If checked, the ExcessHet and InbreedingCoeff annotations will be skipped, which can be important when using force-output-intervals',
+				defaultValue: null
 			},{
 				fieldXtype: 'checkbox',
 				name: 'doCopyInputs',

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java

@@ -636,11 +636,14 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
             }
 
             // NOTE: added to side-step https://github.com/broadinstitute/gatk/issues/7938
-            toolParams.add("-AX");
-            toolParams.add("InbreedingCoeff");
+            if (ctx.getParams().optBoolean("variantCalling.GenotypeGVCFs.skipExcessHetAndInbreeding"))
+            {
+                toolParams.add("-AX");
+                toolParams.add("InbreedingCoeff");
 
-            toolParams.add("-AX");
-            toolParams.add("ExcessHet");
+                toolParams.add("-AX");
+                toolParams.add("ExcessHet");
+            }
 
             if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs.maxGenotypeCount"))
             {