Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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public class LikelihoodRankSumTest extends RankSumTest {
    @Override
    public List<String> getKeyNames() { return Arrays.asList("LikelihoodRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("LikelihoodRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods")); }
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        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("GC"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("GC", 1, VCFHeaderLineType.Integer, "GC content around the variant (see docs for window size details)")); }
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        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("HRun"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("HRun", 1, VCFHeaderLineType.Integer, "Largest Contiguous Homopolymer Run of Variant Allele In Either Direction")); }
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    public List<String> getKeyNames() {
        return Arrays.asList("HaplotypeScore");
    }

    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(new VCFInfoHeaderLine("HaplotypeScore", 1, VCFHeaderLineType.Float, "Consistency of the site with at most two segregating haplotypes"));
    }
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    public List<String> getKeyNames() {
        return Collections.singletonList(FS);
    }

    public List<VCFInfoHeaderLine> getDescriptions() {
        return Collections.singletonList(new VCFInfoHeaderLine(FS, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias"));
    }
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    }

    // return the descriptions used for the VCF INFO meta field
    public List<String> getKeyNames() { return Arrays.asList(MVLR_KEY); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(MVLR_KEY, 1, VCFHeaderLineType.Float, "Mendelian violation likelihood ratio: L[MV] - L[No MV]")); }
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    }

    // return the descriptions used for the VCF INFO meta field
    public List<String> getKeyNames() { return Arrays.asList("TDT"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("TDT", VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Test statistic from Wittkowski transmission disequilibrium test.")); }
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        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("Dels"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Dels", 1, VCFHeaderLineType.Float, "Fraction of Reads Containing Spanning Deletions")); }
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    @Override
    public List<String> getKeyNames() { return Collections.singletonList(INBREEDING_COEFFICIENT_KEY_NAME); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Collections.singletonList(new VCFInfoHeaderLine(INBREEDING_COEFFICIENT_KEY_NAME, 1, VCFHeaderLineType.Float, "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation")); }
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        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("VariantType"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("VariantType", 1, VCFHeaderLineType.String, "Variant type description")); }
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Related Classes of htsjdk.variant.vcf.VCFInfoHeaderLine

  • bcbio.gatk.tools.walkers.annotator.FisherStrand
  • bcbio.gatk.tools.walkers.annotator.GCContent
  • bcbio.variation.annotate.AlleleBalanceConfidenceInterval
  • bcbio.variation.annotate.MostProbableGenotype
  • bcbio.variation.annotate.ReadMeanLen
  • bcbio.variation.annotate.ReadMeanPos
  • bcbio.variation.annotate.ReadPosEndDist
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalance
  • org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts
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