org.bdgenomics.quinine.metrics.contamination

ContaminationEstimator

object ContaminationEstimator extends Serializable

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  10. def estimateContamination(reads: RDD[AlignmentRecord], genotypes: RDD[Genotype], annotations: RDD[DatabaseVariantAnnotation]): ContaminationEstimate

    Estimates inter-sample contamination given reads, prior genotypes, and frequency information.

    Estimates inter-sample contamination given reads, prior genotypes, and frequency information.

    reads

    NGS reads from a sample, to analyze for contamination.

    genotypes

    Data from a prior genotyping study.

    annotations

    Allele frequency annotations.

    returns

    Returns the estimated contamination.

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