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Really don't output VCs with no ALT if * gets dropped #5844

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Mar 28, 2019
Merged

Really don't output VCs with no ALT if * gets dropped #5844

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4 changes: 2 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -387,12 +387,12 @@ private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalculationResult
final boolean isNonRefWhichIsLoneAltAllele = alternativeAlleleCount == 1 && allele.equals(Allele.NON_REF_ALLELE);
final boolean isPlausible = afCalculationResult.isPolymorphicPhredScaledQual(allele, configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING);

siteIsMonomorphic &= !isPlausible;

//it's possible that the upstream deletion that spanned this site was not emitted, mooting the symbolic spanning deletion allele
final boolean isSpuriousSpanningDeletion = GATKVCFConstants.isSpanningDeletion(allele) && !isVcCoveredByDeletion(vc);
final boolean toOutput = (isPlausible || forceKeepAllele(allele) || isNonRefWhichIsLoneAltAllele) && !isSpuriousSpanningDeletion;

siteIsMonomorphic &= !(isPlausible && !isSpuriousSpanningDeletion);

if (toOutput) {
outputAlleles.add(allele);
mleCounts.add(afCalculationResult.getAlleleCountAtMLE(allele));
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6 changes: 4 additions & 2 deletions .../java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngineUnitTest.java
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Expand Up @@ -98,7 +98,8 @@ public void testCalculateGenotypes() {
final VariantContext vcSpanDel = new VariantContextBuilder("test1", "1",2, 2 + refAlleleSpanDel.length() - 1, vcAllelesSpanDel).
genotypes(genotypesSpanDel).make();
final VariantContext vcOut1 = genotypingEngine.calculateGenotypes(vcSpanDel, GenotypeLikelihoodsCalculationModel.INDEL, null);
Assert.assertTrue(vcOut1 == null || !vcOut1.getAlleles().contains(Allele.SPAN_DEL));
//the site is monomorphic, which becomes null
Assert.assertTrue(vcOut1 == null);

final List<Allele> mutliAllelicWithSpanDel = new ArrayList<>(Arrays.asList(refAlleleSpanDel, Allele.SPAN_DEL,
Allele.create("T")));
Expand All @@ -125,7 +126,8 @@ public void testCalculateGenotypes() {
final VariantContext vcMultiWithSpanDel = new VariantContextBuilder("test2", "1",2, 2 + refAlleleSpanDel.length() - 1, mutliAllelicWithSpanDel).
genotypes(regressionGenotypes).make();
final VariantContext vcOut2 = genotypingEngine.calculateGenotypes(vcMultiWithSpanDel, GenotypeLikelihoodsCalculationModel.SNP, null);
Assert.assertTrue(vcOut2 == null || vcOut2.isMonomorphicInSamples());
//low quality T should get dropped, leaving only star, which shouldn't be output
Assert.assertTrue(vcOut2 == null);
}

@Test //test for https://github.com/broadinstitute/gatk/issues/2530
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