org.hammerlab.guacamole.filters.genotype

ReadDepthFilter

object ReadDepthFilter

Filter to remove genotypes where the number of reads at the locus is too low or too high

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  6. def apply(genotypes: RDD[CalledAllele], minReadDepth: Int, maxReadDepth: Int, debug: Boolean = false): RDD[CalledAllele]

    Apply the filter to an RDD of genotypes

    Apply the filter to an RDD of genotypes

    genotypes

    RDD of genotypes to filter

    minReadDepth

    minimum number of reads at locus for this genotype

    maxReadDepth

    maximum number of reads at locus for this genotype

    debug

    if true, compute the count of genotypes after filtering

    returns

    Genotypes with read depth >= minReadDepth and < maxReadDepth

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  23. def withinReadDepthRange(alleleEvidence: AlleleEvidence, minReadDepth: Int, maxReadDepth: Int): Boolean

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