From cb8bc18aeb7780af067f90351566a538fe2f7df8 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 2 Aug 2012 11:41:06 -0400 Subject: [PATCH] Fix for error in HaplotypeCaller. HC has a UG argument collection for the UG engine but some of those arguments aren't appropriate to set. --- .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java | 1 + 1 file changed, 1 insertion(+) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index f5f707690..6bb894323 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -239,6 +239,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem Set samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()); samplesList.addAll( samples ); // initialize the UnifiedGenotyper Engine which is used to call into the exact model + UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP; // the GLmodel isn't used by the HaplotypeCaller but it is dangerous to let the user change this argument UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC.clone(), logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; // low values used for isActive determination only, default/user-specified values used for actual calling UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; // low values used for isActive determination only, default/user-specified values used for actual calling