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 Details

    • 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 Details

    • TargetMetrics

      public TargetMetrics()