From 827be878b4b444f047d1fab5819d3b5b54a7c3ce Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Mon, 6 Feb 2012 11:58:13 -0500 Subject: [PATCH] Bug fix when running UG in GenotypeGivenAlleles mode: if an input site to genotype had no coverage, the output VCF had AC,AF and AN inherited from input VCF, which could have nothing to do with given BAM so numbers could be non-sensical. Now new vc has clear attributes instead of attributes inherited from input VCF. --- .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index aa33d39e3..5cdef6cf5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -252,7 +252,7 @@ public class UnifiedGenotyperEngine { VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles); if ( vcInput == null ) return null; - vc = new VariantContextBuilder(vcInput).source("UG_call").noID().referenceBaseForIndel(ref.getBase()).make(); + vc = new VariantContextBuilder(vcInput).source("UG_call").noID().referenceBaseForIndel(ref.getBase()).attributes(new HashMap()).make(); } else { // deal with bad/non-standard reference bases if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )