Examples with Genotype htsjdk.variant.variantcontext.Genotype used on opensource projects

Example 1 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project gatk by broadinstitute.

the class HomRefBlockUnitTest method testToVariantContext.

@Test
public void testToVariantContext() {
    final VariantContext vc = getVariantContext();
    final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, vc.getAlleles());
    final Genotype genotype1 = gb.GQ(15).DP(6).PL(new int[] { 0, 10, 100 }).make();
    final Genotype genotype2 = gb.GQ(17).DP(10).PL(new int[] { 0, 5, 80 }).make();
    final HomRefBlock block = getHomRefBlock(vc);
    block.add(vc.getEnd(), genotype1);
    block.add(vc.getEnd() + 1, genotype2);
    final VariantContext newVc = block.toVariantContext(SAMPLE_NAME);
    Assert.assertEquals(newVc.getGenotypes().size(), 1);
    final Genotype genotype = newVc.getGenotypes().get(0);
    //dp should be median of the added DPs
    Assert.assertEquals(genotype.getDP(), 8);
    //GQ should have been recalculated with the minPls
    Assert.assertEquals(genotype.getGQ(), 5);
    Assert.assertTrue(genotype.getAlleles().stream().allMatch(a -> a.equals(REF)));
}

Example 2 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project gatk-protected by broadinstitute.

the class HaplotypeCallerSparkIntegrationTest method testFastGenotypeIsSerializable.

@Test
public void testFastGenotypeIsSerializable() {
    Genotype genotype = GenotypeBuilder.create("sample1", Collections.nCopies(2, Allele.create("C", false)));
    SparkTestUtils.roundTripInKryo(genotype, genotype.getClass(), SparkContextFactory.getTestSparkContext().getConf());
}

Example 3 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project gatk by broadinstitute.

the class QualByDepth method annotate.

@Override
public Map<String, Object> annotate(final ReferenceContext ref, final VariantContext vc, final ReadLikelihoods<Allele> likelihoods) {
    Utils.nonNull(vc);
    if (!vc.hasLog10PError()) {
        return Collections.emptyMap();
    }
    final GenotypesContext genotypes = vc.getGenotypes();
    if (genotypes == null || genotypes.isEmpty()) {
        return Collections.emptyMap();
    }
    int depth = 0;
    int ADrestrictedDepth = 0;
    for (final Genotype genotype : genotypes) {
        // we care only about variant calls with likelihoods
        if (!genotype.isHet() && !genotype.isHomVar()) {
            continue;
        }
        // if we have the AD values for this sample, let's make sure that the variant depth is greater than 1!
        if (genotype.hasAD()) {
            final int[] AD = genotype.getAD();
            final int totalADdepth = (int) MathUtils.sum(AD);
            if (totalADdepth != 0) {
                if (totalADdepth - AD[0] > 1) {
                    ADrestrictedDepth += totalADdepth;
                }
                depth += totalADdepth;
            }
        } else if (likelihoods != null) {
            depth += likelihoods.sampleReadCount(likelihoods.indexOfSample(genotype.getSampleName()));
        } else if (genotype.hasDP()) {
            depth += genotype.getDP();
        }
    }
    // if the AD-restricted depth is a usable value (i.e. not zero), then we should use that one going forward
    if (ADrestrictedDepth > 0) {
        depth = ADrestrictedDepth;
    }
    if (depth == 0) {
        return Collections.emptyMap();
    }
    final double qual = -10.0 * vc.getLog10PError();
    double QD = qual / depth;
    // Hack: see note in the fixTooHighQD method below
    QD = fixTooHighQD(QD);
    return Collections.singletonMap(getKeyNames().get(0), String.format("%.2f", QD));
}

Example 4 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project gatk by broadinstitute.

the class SampleList method annotate.

@Override
public Map<String, Object> annotate(final ReferenceContext ref, final VariantContext vc, final ReadLikelihoods<Allele> likelihoods) {
    Utils.nonNull(vc);
    if (vc.isMonomorphicInSamples() || !vc.hasGenotypes()) {
        return Collections.emptyMap();
    }
    final StringBuilder samples = new StringBuilder();
    for (final Genotype genotype : vc.getGenotypesOrderedByName()) {
        if (genotype.isCalled() && !genotype.isHomRef()) {
            if (samples.length() > 0) {
                samples.append(",");
            }
            samples.append(genotype.getSampleName());
        }
    }
    if (samples.length() == 0) {
        return Collections.emptyMap();
    }
    return Collections.singletonMap(getKeyNames().get(0), samples.toString());
}

Example 5 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project gatk by broadinstitute.

the class StrandArtifact method annotate.

@Override
public void annotate(final ReferenceContext ref, final VariantContext vc, final Genotype g, final GenotypeBuilder gb, final ReadLikelihoods<Allele> likelihoods) {
    Utils.nonNull(gb);
    Utils.nonNull(vc);
    Utils.nonNull(likelihoods);
    // do not annotate the genotype fields for normal
    if (g.isHomRef()) {
        return;
    }
    pi.put(NO_ARTIFACT, 0.95);
    pi.put(ART_FWD, 0.025);
    pi.put(ART_REV, 0.025);
    // We use the allele with highest LOD score
    final double[] tumorLods = GATKProtectedVariantContextUtils.getAttributeAsDoubleArray(vc, GATKVCFConstants.TUMOR_LOD_KEY, () -> null, -1);
    final int indexOfMaxTumorLod = MathUtils.maxElementIndex(tumorLods);
    final Allele altAlelle = vc.getAlternateAllele(indexOfMaxTumorLod);
    final Collection<ReadLikelihoods<Allele>.BestAllele<Allele>> bestAlleles = likelihoods.bestAlleles(g.getSampleName());
    final int numFwdAltReads = (int) bestAlleles.stream().filter(ba -> !ba.read.isReverseStrand() && ba.isInformative() && ba.allele.equals(altAlelle)).count();
    final int numRevAltReads = (int) bestAlleles.stream().filter(ba -> ba.read.isReverseStrand() && ba.isInformative() && ba.allele.equals(altAlelle)).count();
    final int numFwdReads = (int) bestAlleles.stream().filter(ba -> !ba.read.isReverseStrand() && ba.isInformative()).count();
    final int numRevReads = (int) bestAlleles.stream().filter(ba -> ba.read.isReverseStrand() && ba.isInformative()).count();
    final int numAltReads = numFwdAltReads + numRevAltReads;
    final int numReads = numFwdReads + numRevReads;
    final EnumMap<StrandArtifactZ, Double> unnormalized_posterior_probabilities = new EnumMap<>(StrandArtifactZ.class);
    final EnumMap<StrandArtifactZ, Double> maximum_a_posteriori_allele_fraction_estimates = new EnumMap<>(StrandArtifactZ.class);
    /*** Compute the posterior probability of ARTIFACT_FWD and ARTIFACT_REV; it's a double integral over f and epsilon ***/
    // the integrand is a polynomial of degree n, where n is the number of reads at the locus
    // thus to integrate exactly with Gauss-Legendre we need (n/2)+1 points
    final int numIntegPointsForAlleleFraction = numReads / 2 + 1;
    final int numIntegPointsForEpsilon = (numReads + ALPHA + BETA - 2) / 2 + 1;
    final double likelihoodForArtifactFwd = IntegrationUtils.integrate2d((f, epsilon) -> getIntegrandGivenArtifact(f, epsilon, numFwdReads, numRevReads, numFwdAltReads, numRevAltReads), 0.0, 1.0, numIntegPointsForAlleleFraction, 0.0, 1.0, numIntegPointsForEpsilon);
    final double likelihoodForArtifactRev = IntegrationUtils.integrate2d((f, epsilon) -> getIntegrandGivenArtifact(f, epsilon, numRevReads, numFwdReads, numRevAltReads, numFwdAltReads), 0.0, 1.0, numIntegPointsForAlleleFraction, 0.0, 1.0, numIntegPointsForEpsilon);
    unnormalized_posterior_probabilities.put(ART_FWD, pi.get(ART_FWD) * likelihoodForArtifactFwd);
    unnormalized_posterior_probabilities.put(ART_REV, pi.get(ART_REV) * likelihoodForArtifactRev);
    /*** Compute the posterior probability of NO_ARTIFACT; evaluate a single integral over the allele fraction ***/
    final double likelihoodForNoArtifact = IntegrationUtils.integrate(f -> getIntegrandGivenNoArtifact(f, numFwdReads, numRevReads, numFwdAltReads, numRevAltReads), 0.0, 1.0, numIntegPointsForAlleleFraction);
    unnormalized_posterior_probabilities.put(NO_ARTIFACT, pi.get(NO_ARTIFACT) * likelihoodForNoArtifact);
    final double[] posterior_probabilities = MathUtils.normalizeFromRealSpace(unnormalized_posterior_probabilities.values().stream().mapToDouble(Double::doubleValue).toArray());
    /*** Compute the maximum a posteriori estimate for allele fraction given strand artifact ***/
    // For a fixed f, integrate the double integral over epsilons. This gives us the likelihood p(x^+, x^- | f, z) for a fixed f, which is proportional to
    // the posterior probability of p(f | x^+, x^-, z)
    final int numSamplePoints = 100;
    final double[] samplePoints = GATKProtectedMathUtils.createEvenlySpacedPoints(0.0, 1.0, numSamplePoints);
    double[] likelihoodsGivenForwardArtifact = new double[numSamplePoints];
    double[] likelihoodsGivenReverseArtifact = new double[numSamplePoints];
    for (int i = 0; i < samplePoints.length; i++) {
        final double f = samplePoints[i];
        likelihoodsGivenForwardArtifact[i] = IntegrationUtils.integrate(epsilon -> getIntegrandGivenArtifact(f, epsilon, numFwdReads, numRevReads, numFwdAltReads, numRevAltReads), 0.0, 1.0, numIntegPointsForEpsilon);
        likelihoodsGivenReverseArtifact[i] = IntegrationUtils.integrate(epsilon -> getIntegrandGivenArtifact(f, epsilon, numRevReads, numFwdReads, numRevAltReads, numFwdAltReads), 0.0, 1.0, numIntegPointsForEpsilon);
    }
    final int maxAlleleFractionIndexFwd = MathUtils.maxElementIndex(likelihoodsGivenForwardArtifact);
    final int maxAlleleFractionIndexRev = MathUtils.maxElementIndex(likelihoodsGivenReverseArtifact);
    maximum_a_posteriori_allele_fraction_estimates.put(ART_FWD, samplePoints[maxAlleleFractionIndexFwd]);
    maximum_a_posteriori_allele_fraction_estimates.put(ART_REV, samplePoints[maxAlleleFractionIndexRev]);
    // In the absence of strand artifact, MAP estimate for f reduces to the sample alt allele fraction
    maximum_a_posteriori_allele_fraction_estimates.put(NO_ARTIFACT, (double) numAltReads / numReads);
    gb.attribute(POSTERIOR_PROBABILITIES_KEY, posterior_probabilities);
    gb.attribute(MAP_ALLELE_FRACTIONS_KEY, maximum_a_posteriori_allele_fraction_estimates.values().stream().mapToDouble(Double::doubleValue).toArray());
}