diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java index db3a86045..581b3b6a0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java @@ -127,7 +127,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel { HashMap attributes = new HashMap(); attributes.put(VCFConstants.DEPTH_KEY, getFilteredDepth(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup())); - 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, AFbasedGenotype.second, null, attributes, false)); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java index 3d21a6b6e..833ed1423 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java @@ -49,6 +49,8 @@ import java.io.PrintStream; @By(DataSource.REFERENCE) @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250) public class UnifiedGenotyperV2 extends LocusWalker implements TreeReducible { + public static final String DEFAULT_GENOTYPE_LIKELIHOODS_KEY = VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY; + @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); @@ -156,7 +158,7 @@ public class UnifiedGenotyperV2 extends LocusWalker