Skip GATK annotations to avoid broadinstitute/gatk#7938

BimberLab · Aug 9, 2022 · 2d1adc3 · 2d1adc3
1 parent e376908
commit 2d1adc3
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
@@ -448,6 +448,13 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
                 toolParams.add(ctx.getParams().get("variantCalling.GenotypeGVCFs.stand_call_conf").toString());
             }
 
+            // NOTE: added to side-step https://github.com/broadinstitute/gatk/issues/7938
+            toolParams.add("-AX");
+            toolParams.add("InbreedingCoeff");
+
+            toolParams.add("-AX");
+            toolParams.add("ExcessHet");
+
             if (ctx.getParams().get("variantCalling.GenotypeGVCFs.maxGenotypeCount") != null)
             {
                 toolParams.add("-max-genotype-count");