object ReviewConsensusVariants

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  1. case class ConsensusVariantReviewInfo (chrom: String, pos: Int, ref: String, genotype: String, filters: String, A: Int, C: Int, G: Int, T: Int, N: Int, consensus_read: String, consensus_insert: String, consensus_call: String, consensus_qual: Int, a: Int, c: Int, g: Int, t: Int, n: Int) extends Metric with Product with Serializable

    Metric class that is used to output detailed information on each consensus read that carries a variant allele

    Metric class that is used to output detailed information on each consensus read that carries a variant allele

    chrom

    the chromosome on which the variant exists

    pos

    the position of the variant

    ref

    the reference allele at the position

    genotype

    the genotype of the sample in question

    filters

    the set of filters applied to the variant in the VCF

    A

    the count of A observations at the variant locus

    C

    the count of C observations at the variant locus

    G

    the count of G observations at the variant locus

    T

    the count of T observations at the variant locus

    N

    the count of N observations at the variant locus

    consensus_read

    the consensus read name for which the following fields contain values

    consensus_insert

    a description of the insert that generated the consensus read

    consensus_call

    the base call from the consensus read

    consensus_qual

    the quality score from the consensus read

    a

    the number of As in raw-reads contributing to the consensus base call at the variant site

    c

    the number of Cs in raw-reads contributing to the consensus base call at the variant site

    g

    the number of Gs in raw-reads contributing to the consensus base call at the variant site

    t

    the number of Ts in raw-reads contributing to the consensus base call at the variant site

    n

    the number of Ns in raw-reads contributing to the consensus base call at the variant site

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