diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 2b46414a8..5c7da82d0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -364,7 +364,7 @@ public class VariantContextAdaptors { long end = hapmap.getEnd(); if ( deletionLength > 0 ) - end += deletionLength; + end += (deletionLength - 1); VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).make(); return vc; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 5f80f77a4..059e9c5fb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -160,7 +160,7 @@ public class VariantsToVCF extends RodWalker { Map alleleMap = new HashMap(2); alleleMap.put(RawHapMapFeature.DELETION, Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion())); - alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion())); + alleleMap.put(RawHapMapFeature.INSERTION, Allele.create((char)ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion())); hapmap.setActualAlleles(alleleMap); // also, use the correct positioning for insertions