diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java index f31595f75..48024ed33 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java @@ -257,7 +257,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel { attributes.put(VCFConstants.GENOTYPE_QUALITY_KEY,String.format("%4.2f", 10*qual)); - GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods()); + GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods(), UnifiedGenotyperV2.DEFAULT_GENOTYPE_LIKELIHOODS_KEY); attributes.put(likelihoods.getKey(), likelihoods.getAsString()); calls.put(sample, new Genotype(sample, myAlleles, qual, null, attributes, false)); diff --git a/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java index a777087c1..5746b03b5 100755 --- a/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java +++ b/java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java @@ -176,7 +176,7 @@ public class VCFUtils { if ( glType == VCFConstants.GENOTYPE_LIKELIHOODS_KEY ) result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic")); else if ( glType == VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY ) - result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic")); + result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic")); else throw new ReviewedStingException("Unexpected GL type " + glType);