Class TargetMetrics


  • @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public class TargetMetrics
    extends TargetMetricsBase
    TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA). TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics.
    • Field Detail

      • PROBE_SET

        public String PROBE_SET
        The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
      • PROBE_TERRITORY

        public long PROBE_TERRITORY
        The number of unique bases covered by the intervals of all probes in the probe set
      • ON_PROBE_BASES

        public long ON_PROBE_BASES
        The number of PF aligned probed bases that mapped to a baited region of the genome.
      • NEAR_PROBE_BASES

        public long NEAR_PROBE_BASES
        The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.
      • OFF_PROBE_BASES

        public long OFF_PROBE_BASES
        The number of PF aligned bases that mapped to neither on or near a probe.
      • PCT_SELECTED_BASES

        public double PCT_SELECTED_BASES
        The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
      • PCT_OFF_PROBE

        public double PCT_OFF_PROBE
        The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
      • ON_PROBE_VS_SELECTED

        public double ON_PROBE_VS_SELECTED
        The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
      • MEAN_PROBE_COVERAGE

        public double MEAN_PROBE_COVERAGE
        The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
      • FOLD_ENRICHMENT

        public double FOLD_ENRICHMENT
        The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
    • Constructor Detail

      • TargetMetrics

        public TargetMetrics()