Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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        return map;
    }

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

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBase", 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup")); }
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    }

    public List<String> getKeyNames() { return Arrays.asList("ABHet","ABHom","OND"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ABHet", 1, VCFHeaderLineType.Float, "Allele Balance for heterozygous calls (ref/(ref+alt))"),
            new VCFInfoHeaderLine("ABHom", 1, VCFHeaderLineType.Float, "Allele Balance for homozygous calls (A/(A+O)) where A is the allele (ref or alt) and O is anything other"),
            new VCFInfoHeaderLine("OND", 1, VCFHeaderLineType.Float, "Overall non-diploid ratio (alleles/(alleles+non-alleles))")); }
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        return map;
    }

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

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 3, VCFHeaderLineType.Float, "3-tuple: <fraction of reads with MQ=0>,<fraction of reads with MQ<=10>,<total number of reads>")); }
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        return map;
    }

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

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseCounts", 4, VCFHeaderLineType.Integer, "Counts of each base")); }
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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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