Class TheoreticalSensitivityMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.TheoreticalSensitivityMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class TheoreticalSensitivityMetrics extends htsjdk.samtools.metrics.MetricBase
TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation. These metrics are intended to estimate the achievable sensitivity (for a particular log odds threshold) of somatic calls for a particular depth and base quality score distribution.
  • Field Details

    • ALLELE_FRACTION

      public double ALLELE_FRACTION
      The allele fraction which theoretical sensitivity is calculated for.
    • THEORETICAL_SENSITIVITY

      public double THEORETICAL_SENSITIVITY
      Estimation of sensitivity at a particular allele fraction.
    • THEORETICAL_SENSITIVITY_Q

      public int THEORETICAL_SENSITIVITY_Q
      Phred-scaled value of 1-THEORETICAL_SENSITIVITY.
    • LOG_ODDS_THRESHOLD

      public double LOG_ODDS_THRESHOLD
      Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.
    • SAMPLE_SIZE

      public int SAMPLE_SIZE
      Number of samples drawn at each depth in the depth distribution. Larger values allow for increased precision at the cost of compute time.
  • Constructor Details

    • TheoreticalSensitivityMetrics

      public TheoreticalSensitivityMetrics()