Fixed M2 bug where triallelic normal artifacts were sometimes hidden from filtering

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java

@@ -26,7 +26,7 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection
     public static final String GERMLINE_RESOURCE_LONG_NAME = "germline-resource";
     public static final String DEFAULT_AF_LONG_NAME = "af-of-alleles-not-in-resource";
     public static final String DEFAULT_AF_SHORT_NAME = "default-af";
-    public static final String EMISSION_LOG_LONG_NAME = "tumor-lod-to-emit";
+    public static final String EMISSION_LOD_LONG_NAME = "tumor-lod-to-emit";
     public static final String EMISSION_LOG_SHORT_NAME = "emit-lod";
     public static final String INITIAL_TUMOR_LOD_LONG_NAME = "initial-tumor-lod";
     public static final String INITIAL_TUMOR_LOD_SHORT_NAME = "init-lod";
@@ -105,14 +105,14 @@ public double getDefaultAlleleFrequency() {
      * Default setting of 3 is permissive and will emit some amount of negative training data that 
      * {@link FilterMutectCalls} should then filter.
      */
-    @Argument(fullName = EMISSION_LOG_LONG_NAME, shortName = EMISSION_LOG_SHORT_NAME, optional = true, doc = "LOD threshold to emit tumor variant to VCF.")
-    public double emissionLodThreshold = 3.0;
+    @Argument(fullName = EMISSION_LOD_LONG_NAME, shortName = EMISSION_LOG_SHORT_NAME, optional = true, doc = "LOD threshold to emit tumor variant to VCF.")
+    public double emissionLod = 3.0;
 
     /**
      * Only variants with estimated tumor LODs exceeding this threshold will be considered active.
      */
     @Argument(fullName = INITIAL_TUMOR_LOD_LONG_NAME, shortName = INITIAL_TUMOR_LOD_SHORT_NAME, optional = true, doc = "LOD threshold to consider pileup active.")
-    public double initialTumorLodThreshold = 2.0;
+    public double initialTumorLod = 2.0;
 
     /**
      * In tumor-only mode, we discard variants with population allele frequencies greater than this threshold.
@@ -140,7 +140,7 @@ public double getDefaultAlleleFrequency() {
      * but may also increase calling false positive, i.e. germline, variants.
      */
     @Argument(fullName = NORMAL_LOD_LONG_NAME, optional = true, doc = "LOD threshold for calling normal variant non-germline.")
-    public double normalLodThreshold = 2.2;
+    public double normalLod = 2.2;
 
     /**
      * Two or more phased substitutions separated by this distance or less are merged into MNPs.

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java

@@ -237,7 +237,7 @@ public ActivityProfileState isActive(final AlignmentContext context, final Refer
         final double tumorLog10Odds = -QualityUtils.qualToErrorProbLog10(tumorAltCountAndQualSum.getSecond()) +
                 MathUtils.log10Factorial(tumorAltCount) + MathUtils.log10Factorial(tumorRefCount) - MathUtils.log10Factorial(tumorPileup.size() + 1);
 
-        if (tumorLog10Odds < MTAC.initialTumorLodThreshold) {
+        if (tumorLog10Odds < MTAC.initialTumorLod) {
             return new ActivityProfileState(refInterval, 0.0);
         } else if (hasNormal() && !MTAC.genotypeGermlineSites) {
             final ReadPileup normalPileup = pileup.getPileupForSample(normalSample, header);

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java

@@ -126,30 +126,39 @@ public CalledHaplotypes callMutations(
             final Optional<PerAlleleCollection<Double>> normalLog10Odds = getForNormal(() -> diploidAltLog10Odds(log10NormalMatrix.get()));
             final Optional<PerAlleleCollection<Double>> normalArtifactLog10Odds = getForNormal(() -> somaticLog10Odds(log10NormalMatrix.get()));
 
-            final Set<Allele> allelesConsistentWithGivenAlleles = getAllelesConsistentWithGivenAlleles(givenAlleles, loc, mergedVC);
-            final List<Allele> somaticAltAlleles = mergedVC.getAlternateAlleles().stream()
-                    .filter(allele -> allelesConsistentWithGivenAlleles.contains(allele) ||
-                            ((tumorLog10Odds.getAlt(allele) > MTAC.emissionLodThreshold) &&
-                            (!hasNormal || MTAC.genotypeGermlineSites || normalLog10Odds.get().getAlt(allele) > MTAC.normalLodThreshold)))
+            final Set<Allele> forcedAlleles = getAllelesConsistentWithGivenAlleles(givenAlleles, loc, mergedVC);
+
+            final List<Allele> tumorAltAlleles = mergedVC.getAlternateAlleles().stream()
+                    .filter(allele -> forcedAlleles.contains(allele) || tumorLog10Odds.getAlt(allele) > MTAC.emissionLod)
                     .collect(Collectors.toList());
-            final List<Allele> allSomaticAlleles = ListUtils.union(Arrays.asList(mergedVC.getReference()), somaticAltAlleles);
-            if (somaticAltAlleles.isEmpty()) {
+
+            final long somaticAltCount = tumorAltAlleles.stream()
+                    .filter(allele -> forcedAlleles.contains(allele) || !hasNormal || MTAC.genotypeGermlineSites || normalLog10Odds.get().getAlt(allele) > MTAC.normalLod)
+                    .count();
+
+            // if every alt allele is germline, skip this variant.  However, if some alt alleles are germline and others
+            // are not we emit them all so that the filtering engine can see them
+            if (somaticAltCount == 0) {
                 continue;
             }
 
-            final LikelihoodMatrix<Allele> subsettedLog10TumorMatrix = new SubsettedLikelihoodMatrix<>(log10TumorMatrix, allSomaticAlleles);
+
+            final List<Allele> allAllelesToEmit = ListUtils.union(Arrays.asList(mergedVC.getReference()), tumorAltAlleles);
+
+
+            final LikelihoodMatrix<Allele> subsettedLog10TumorMatrix = new SubsettedLikelihoodMatrix<>(log10TumorMatrix, allAllelesToEmit);
             final Optional<LikelihoodMatrix<Allele>> subsettedLog10NormalMatrix =
-                    getForNormal(() -> new SubsettedLikelihoodMatrix<>(log10NormalMatrix.get(), allSomaticAlleles));
+                    getForNormal(() -> new SubsettedLikelihoodMatrix<>(log10NormalMatrix.get(), allAllelesToEmit));
 
-            final Map<String, Object> populationAFAnnotation = GermlineProbabilityCalculator.getPopulationAFAnnotation(featureContext.getValues(MTAC.germlineResource, loc), somaticAltAlleles, MTAC.getDefaultAlleleFrequency());
+            final Map<String, Object> populationAFAnnotation = GermlineProbabilityCalculator.getPopulationAFAnnotation(featureContext.getValues(MTAC.germlineResource, loc), tumorAltAlleles, MTAC.getDefaultAlleleFrequency());
 
             final VariantContextBuilder callVcb = new VariantContextBuilder(mergedVC)
-                    .alleles(allSomaticAlleles)
+                    .alleles(allAllelesToEmit)
                     .attributes(populationAFAnnotation)
-                    .attribute(GATKVCFConstants.TUMOR_LOD_KEY, somaticAltAlleles.stream().mapToDouble(tumorLog10Odds::getAlt).toArray());
+                    .attribute(GATKVCFConstants.TUMOR_LOD_KEY, tumorAltAlleles.stream().mapToDouble(tumorLog10Odds::getAlt).toArray());
 
-            normalLog10Odds.ifPresent(values -> callVcb.attribute(GATKVCFConstants.NORMAL_LOD_KEY, values.asDoubleArray(somaticAltAlleles)));
-            normalArtifactLog10Odds.ifPresent(values -> callVcb.attribute(GATKVCFConstants.NORMAL_ARTIFACT_LOD_ATTRIBUTE, values.asDoubleArray(somaticAltAlleles)));
+            normalLog10Odds.ifPresent(values -> callVcb.attribute(GATKVCFConstants.NORMAL_LOD_KEY, values.asDoubleArray(tumorAltAlleles)));
+            normalArtifactLog10Odds.ifPresent(values -> callVcb.attribute(GATKVCFConstants.NORMAL_ARTIFACT_LOD_ATTRIBUTE, values.asDoubleArray(tumorAltAlleles)));
 
             if (!featureContext.getValues(MTAC.pon, mergedVC.getStart()).isEmpty()) {
                 callVcb.attribute(GATKVCFConstants.IN_PON_VCF_ATTRIBUTE, true);