diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java index 476fe36ae28..e4504398998 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java @@ -176,7 +176,7 @@ public CalledHaplotypes callMutations( if (hasNormal) { callVcb.attribute(GATKVCFConstants.NORMAL_ARTIFACT_LOG_10_ODDS_KEY, - Arrays.stream(normalArtifactLogOdds.asDoubleArray(tumorAltAlleles)).map(x->-MathUtils.logToLog10(x)).toArray()); + Arrays.stream(normalArtifactLogOdds.asDoubleArray(tumorAltAlleles)).map(x->MathUtils.logToLog10(x)).toArray()); callVcb.attribute(GATKVCFConstants.NORMAL_LOG_10_ODDS_KEY, Arrays.stream(normalLogOdds.asDoubleArray(tumorAltAlleles)).map(MathUtils::logToLog10).toArray()); } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/NormalArtifactFilter.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/NormalArtifactFilter.java index 560ec648657..5ec7a9a2ada 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/NormalArtifactFilter.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/NormalArtifactFilter.java @@ -45,7 +45,7 @@ public double calculateErrorProbability(final VariantContext vc, final Mutect2Fi return 0.0; } - final double[] normalArtifactNegativeLogOdds = MathUtils.applyToArrayInPlace(VariantContextGetters.getAttributeAsDoubleArray(vc, GATKVCFConstants.NORMAL_ARTIFACT_LOG_10_ODDS_KEY), MathUtils::log10ToLog); + final double[] normalArtifactNegativeLogOdds = MathUtils.applyToArrayInPlace(VariantContextGetters.getAttributeAsDoubleArray(vc, GATKVCFConstants.NORMAL_ARTIFACT_LOG_10_ODDS_KEY), x -> -MathUtils.log10ToLog(x)); final double normalArtifactProbability = filteringEngine.posteriorProbabilityOfNormalArtifact(normalArtifactNegativeLogOdds[indexOfMaxTumorLod]); // the normal artifact log odds misses artifacts whose support in the normal consists entirely of low base quality reads diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java index 21d48aeb104..0e00e84cc57 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java @@ -235,7 +235,7 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf addInfoLine(new VCFInfoHeaderLine(STRAND_QUAL_KEY, 1, VCFHeaderLineType.Integer, "Phred-scaled quality of strand bias artifact")); addInfoLine(new VCFInfoHeaderLine(CONTAMINATION_QUAL_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled qualities that alt allele are not due to contamination")); addInfoLine(new VCFInfoHeaderLine(READ_ORIENTATION_QUAL_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled qualities that alt allele are not due to read orientation artifact")); - addInfoLine(new VCFInfoHeaderLine(NORMAL_ARTIFACT_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Negative log 10 odds of artifact in normal with same allele fraction as tumor")); + addInfoLine(new VCFInfoHeaderLine(NORMAL_ARTIFACT_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Log 10 odds of artifact in normal with same allele fraction as tumor")); addInfoLine(new VCFInfoHeaderLine(ORIGINAL_CONTIG_MISMATCH_KEY, 1, VCFHeaderLineType.Integer, "Number of alt reads whose original alignment doesn't match the current contig.")); addInfoLine(new VCFInfoHeaderLine(N_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Count of N bases in the pileup")); addInfoLine(new VCFInfoHeaderLine(AS_UNIQUE_ALT_READ_SET_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Number of reads with unique start and mate end positions for each alt at a variant site"));