diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java index 751386ed2..f0042a94d 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java @@ -344,6 +344,9 @@ public class VCFWriter { if ( allowedGenotypeAttributeKeys == null || allowedGenotypeAttributeKeys.contains(key) ) vcfGenotypeAttributeKeys.add(key); } + } else if ( header.hasGenotypingData() ) { + // this needs to be done in case all samples are no-calls + vcfGenotypeAttributeKeys.add(VCFGenotypeRecord.GENOTYPE_KEY); } String genotypeFormatString = Utils.join(GENOTYPE_FIELD_SEPARATOR, vcfGenotypeAttributeKeys);