VAFHistogram

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6. object Caller extends SparkCommand[Arguments]

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8. def buildMixtureModel(variantLoci: RDD[VariantLocus], numClusters: Int, maxIterations: Int = 50, convergenceTol: Double = 1e-2): GaussianMixtureModel

   Fit a Gaussian mixture model to the distribution of variant allele frequencies

   Fit a Gaussian mixture model to the distribution of variant allele frequencies

   variantLoci

   RDD of loci with variant allele frequency > 0

   numClusters

   Number of Gaussian distributions to fit

   maxIterations

   Maximum number of iterations to run EM

   convergenceTol

   Largest change in log-likelihood before convergence

   returns

   GaussianMixtureModel

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13. def generateVAFHistograms(variantAlleleFrequencies: RDD[VariantLocus], bins: Int): Map[SampleId, Vector[(Int, Long)]]

    Generates a count of loci in each variant allele frequency bins

    Generates a count of loci in each variant allele frequency bins

    variantAlleleFrequencies

    RDD of loci with variant allele frequency > 0

    bins

    Number of bins to group the VAFs into

    returns

    Map of rounded variant allele frequency to number of loci with that value

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22. def variantLociFromReads(sampleNames: PerSample[SampleName], partitionedReads: PartitionedReads, reference: ReferenceGenome, samplePercent: Int = 100, minReadDepth: Int = 0, minVariantAlleleFrequency: Int = 0, printStats: Boolean = false): (RDD[VariantLocus], Map[SampleId, Long])

    Find all non-reference loci in the sample

    Find all non-reference loci in the sample

    sampleNames

    names of underlying samples comprising partitionedReads

    partitionedReads

    partitioned, mapped reads

    reference

    genome

    samplePercent

    Percent of non-reference loci to use for descriptive statistics

    minReadDepth

    Minimum read depth before including variant allele frequency

    minVariantAlleleFrequency

    Minimum variant allele frequency to include

    printStats

    Print descriptive statistics for the variant allele frequency distribution

    returns

    RDD of VariantLocus, which contain the locus and non-zero variant allele frequency

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