Class TargetedPcrMetrics


  • public class TargetedPcrMetrics
    extends TargetMetricsBase
    Metrics class for the analysis of reads obtained from targeted pcr experiments e.g. the TruSeq Custom Amplicon (TSCA) kit (Illumina).
    • Field Detail

      • CUSTOM_AMPLICON_SET

        public String CUSTOM_AMPLICON_SET
        The name of the amplicon set used in this metrics collection run
      • AMPLICON_TERRITORY

        public long AMPLICON_TERRITORY
        The number of unique bases covered by the intervals of all amplicons in the amplicon set
      • ON_AMPLICON_BASES

        public long ON_AMPLICON_BASES
        The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
      • NEAR_AMPLICON_BASES

        public long NEAR_AMPLICON_BASES
        The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
      • OFF_AMPLICON_BASES

        public long OFF_AMPLICON_BASES
        The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
      • PCT_AMPLIFIED_BASES

        public double PCT_AMPLIFIED_BASES
        The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
      • PCT_OFF_AMPLICON

        public double PCT_OFF_AMPLICON
        The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
      • ON_AMPLICON_VS_SELECTED

        public double ON_AMPLICON_VS_SELECTED
        The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
      • MEAN_AMPLICON_COVERAGE

        public double MEAN_AMPLICON_COVERAGE
        The mean read coverage of all amplicon regions in the experiment.
      • FOLD_ENRICHMENT

        public double FOLD_ENRICHMENT
        The fold by which the amplicon region has been amplified above genomic background.
    • Constructor Detail

      • TargetedPcrMetrics

        public TargetedPcrMetrics()