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fixed a bug where normal p value argument in FilterMutectCalls was static #5982

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Jun 6, 2019
Merged

fixed a bug where normal p value argument in FilterMutectCalls was static #5982

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2 changes: 1 addition & 1 deletion ...broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,7 @@ public double getLogIndelPrior() {
public double initialLogPriorOfVariantVersusArtifact = DEFAULT_INITIAL_LOG_PRIOR_OF_VARIANT_VERSUS_ARTIFACT;

@Argument(fullName = NORMAL_P_VALUE_THRESHOLD_LONG_NAME, optional = true, doc = "P value threshold for normal artifact filter")
public static final double normalPileupPValueThreshold = DEFAULT_NORMAL_P_VALUE_THRESHOLD;
public double normalPileupPValueThreshold = DEFAULT_NORMAL_P_VALUE_THRESHOLD;

@Argument(fullName = MIN_POLYMERASE_SLIPPAGE_LENGTH, optional = true, doc = "Minimum number of reference bases in an STR to suspect polymerase slippage")
public int minSlippageLength = DEFAULT_MIN_SLIPPAGE_LENGTH;
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2 changes: 1 addition & 1 deletion .../org/broadinstitute/hellbender/tools/walkers/mutect/filtering/Mutect2FilteringEngine.java
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Expand Up @@ -206,7 +206,7 @@ private void buildFiltersList(final M2FiltersArgumentCollection MTFAC) {
filters.add(new StrandArtifactFilter());
filters.add(new ContaminationFilter(MTFAC.contaminationTables, MTFAC.contaminationEstimate));
filters.add(new PanelOfNormalsFilter());
filters.add(new NormalArtifactFilter());
filters.add(new NormalArtifactFilter(MTFAC.normalPileupPValueThreshold));
filters.add(new NRatioFilter(MTFAC.nRatio));
filters.add(new StrictStrandBiasFilter(MTFAC.minReadsOnEachStrand));
filters.add(new ReadPositionFilter(MTFAC.minMedianReadPosition));
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7 changes: 6 additions & 1 deletion ...va/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/NormalArtifactFilter.java
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Expand Up @@ -16,6 +16,11 @@ public class NormalArtifactFilter extends Mutect2VariantFilter {
private static final double MIN_NORMAL_ARTIFACT_RATIO = 0.1; // don't call normal artifact if allele fraction in normal is much smaller than allele fraction in tumor
private static final int IMPUTED_NORMAL_BASE_QUALITY = 30; // only used if normal base quality annotation fails somehow

private final double normalPileupPValueThreshold;
public NormalArtifactFilter(final double normalPileupPValueThreshold) {
this.normalPileupPValueThreshold = normalPileupPValueThreshold;
}

@Override
public ErrorType errorType() { return ErrorType.ARTIFACT; }

Expand Down Expand Up @@ -50,7 +55,7 @@ public double calculateErrorProbability(final VariantContext vc, final Mutect2Fi
final double normalPValue = 1 - new BinomialDistribution(null, normalDepth, QualityUtils.qualToErrorProb(medianRefBaseQuality))
.cumulativeProbability(normalAltDepth - 1);

return normalPValue < M2FiltersArgumentCollection.normalPileupPValueThreshold ? 1.0 : normalArtifactProbability;
return normalPValue < normalPileupPValueThreshold ? 1.0 : normalArtifactProbability;
}

@Override
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