Class TheoreticalSensitivityMetrics


  • 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 Detail

      • 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 Detail

      • TheoreticalSensitivityMetrics

        public TheoreticalSensitivityMetrics()