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: Char, consensus_qual: Int, a: Int, c: Int, g: Int, t: Int, n: Int) extends Metric with Product with Serializable

    Detailed information produced by ReviewConsensusVariants on variants called in consensus reads.

    Detailed information produced by ReviewConsensusVariants on variants called in consensus reads. Each row contains information about a consensus _read_ that carried a variant or non-reference allele at a particular variant site.

    The first 10 columns (up to N) contain information about the variant site and are repeated for each consensus read reported at that site. The remaining fields are specific to the consensus read.

    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 across all consensus reads.

    C

    The count of C observations at the variant locus across all consensus reads.

    G

    The count of G observations at the variant locus across all consensus reads.

    T

    The count of T observations at the variant locus across all consensus reads.

    N

    The count of N observations at the variant locus across all consensus reads.

    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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