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normal artifact lod is now defined without the extra minus sign #8668

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merged 2 commits into from
Jan 30, 2024
Merged

normal artifact lod is now defined without the extra minus sign #8668

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9f287f2
normal artifact lod is now defined without the extra minus sign
davidbenjamin Jan 29, 2024
a757398
fixed an exact match test
davidbenjamin Jan 30, 2024
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2 changes: 1 addition & 1 deletion ...main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java
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Expand Up @@ -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());
}
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2 changes: 1 addition & 1 deletion ...va/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/NormalArtifactFilter.java
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
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Expand Up @@ -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"));
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