org.bdgenomics.quinine.metrics.targeted

PanelStats

object PanelStats extends Serializable

Companion object for generating statistics about a targeted sequencing panel.

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  6. def apply(reads: RDD[AlignmentRecord], targets: RDD[Feature], bait: RDD[Feature], panelName: String, baseQualThreshold: Int, mappingQualThreshold: Int): PanelStats

    Computes statistics for reads sequenced with a targeted sequencing protocol.

    Computes statistics for reads sequenced with a targeted sequencing protocol.

    reads

    The reads sequenced using this panel.

    targets

    The areas targeted for sequencing using this panel.

    bait

    The bait used for hybrid capture.

    panelName

    The name of this panel.

    baseQualThreshold

    The threshold used for characterizing a base as a high/low quality base.

    mappingQualThreshold

    The threshold used for characterizing a read as being well/poorly mapped.

    returns

    Returns a PanelStats instance that prints the statistics nicely.

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