diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java b/java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java index 3d32ef27d..7db48b5fb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/vcf/VCFCombine.java @@ -204,6 +204,8 @@ public class VCFCombine extends RodWalker { set = priority2 + "-filteredInOther"; call = vcf2; } + } else { + set = priority1 + "-filteredAndNoCall"; } } else { // good call if ( vcf2 != null ) {