Example #1
0
  @Override
  public Map<String, Object> annotate(
      final RefMetaDataTracker tracker,
      final AnnotatorCompatible walker,
      final ReferenceContext ref,
      final Map<String, AlignmentContext> stratifiedContexts,
      final VariantContext vc,
      final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {

    final GenotypesContext genotypes = vc.getGenotypes();
    if (genotypes == null || genotypes.size() < MIN_SAMPLES) {
      if (!warningLogged) {
        logger.warn("Too few genotypes");
        warningLogged = true;
      }
      return null;
    }

    int refCount = 0;
    int hetCount = 0;
    int homCount = 0;
    for (final Genotype g : genotypes) {
      if (g.isNoCall()) continue;

      // TODO - fix me:
      // Right now we just ignore genotypes that are not confident, but this throws off
      //  our HW ratios.  More analysis is needed to determine the right thing to do when
      //  the genotyper cannot decide whether a given sample is het or hom var.
      if (g.getLog10PError() > MIN_LOG10_PERROR) continue;

      if (g.isHomRef()) refCount++;
      else if (g.isHet()) hetCount++;
      else homCount++;
    }

    if (refCount + hetCount + homCount == 0) return null;

    double pvalue = HardyWeinbergCalculation.hwCalculate(refCount, hetCount, homCount);
    // System.out.println(refCount + " " + hetCount + " " + homCount + " " + pvalue);
    Map<String, Object> map = new HashMap<>();
    map.put(getKeyNames().get(0), String.format("%.1f", QualityUtils.phredScaleErrorRate(pvalue)));
    return map;
  }
  private VariantContext makeVC() {
    final GenotypesContext testGC = GenotypesContext.create(2);
    final Allele refAllele = Allele.create("A", true);
    final Allele altAllele = Allele.create("T");

    return (new VariantContextBuilder())
        .alleles(Arrays.asList(refAllele, altAllele))
        .chr("1")
        .start(15L)
        .stop(15L)
        .genotypes(testGC)
        .make();
  }
Example #3
0
  @Test
  public void testFixReverseComplementedGenotypes() {

    final Allele refA = Allele.create("A", true);
    final Allele altC = Allele.create("C", false);
    final GenotypesContext originalGenotypes = GenotypesContext.create(3);
    originalGenotypes.add(new GenotypeBuilder("homref").alleles(Arrays.asList(refA, refA)).make());
    originalGenotypes.add(new GenotypeBuilder("het").alleles(Arrays.asList(refA, altC)).make());
    originalGenotypes.add(new GenotypeBuilder("homvar").alleles(Arrays.asList(altC, altC)).make());

    final Allele refT = Allele.create("T", true);
    final Allele altG = Allele.create("G", false);
    final GenotypesContext expectedGenotypes = GenotypesContext.create(3);
    expectedGenotypes.add(new GenotypeBuilder("homref").alleles(Arrays.asList(refT, refT)).make());
    expectedGenotypes.add(new GenotypeBuilder("het").alleles(Arrays.asList(refT, altG)).make());
    expectedGenotypes.add(new GenotypeBuilder("homvar").alleles(Arrays.asList(altG, altG)).make());

    final Map<Allele, Allele> reverseComplementAlleleMap = new HashMap<Allele, Allele>(2);
    reverseComplementAlleleMap.put(refA, refT);
    reverseComplementAlleleMap.put(altC, altG);
    final GenotypesContext actualGenotypes =
        LiftoverVcf.fixGenotypes(originalGenotypes, reverseComplementAlleleMap);

    for (final String sample : Arrays.asList("homref", "het", "homvar")) {
      final List<Allele> expected = expectedGenotypes.get(sample).getAlleles();
      final List<Allele> actual = actualGenotypes.get(sample).getAlleles();
      Assert.assertEquals(expected.get(0), actual.get(0));
      Assert.assertEquals(expected.get(1), actual.get(1));
    }
  }