Package picard.analysis.directed

Class TargetedPcrMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.directed.PanelMetricsBase
picard.analysis.directed.TargetMetricsBase
picard.analysis.directed.TargetedPcrMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") 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 Details

    • 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 Details

    • TargetedPcrMetrics

      public TargetedPcrMetrics()