Package picard.analysis.artifacts

Class SequencingArtifactMetrics.BaitBiasDetailMetrics

  • Enclosing class:
    SequencingArtifactMetrics
    public static class SequencingArtifactMetrics.BaitBiasDetailMetrics
extends htsjdk.samtools.metrics.MetricBase
    Bait bias artifacts broken down by context.

    • Field Summary

      Fields 
      Modifier and Type Field Description
      char ALT_BASE
      The (upper-case) alternative base that is called as a result of DNA damage.
      String CONTEXT
      The sequence context to which the analysis is constrained.
      double ERROR_RATE
      The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
      long FWD_CXT_ALT_BASES
      The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
      long FWD_CXT_REF_BASES
      The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
      double FWD_ERROR_RATE
      The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).
      String LIBRARY
      The name of the library being assayed.
      double QSCORE
      The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
      char REF_BASE
      The (upper-case) original base on the reference strand.
      long REV_CXT_ALT_BASES
      The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
      long REV_CXT_REF_BASES
      The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
      double REV_ERROR_RATE
      The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
      String SAMPLE_ALIAS  

    • Field Detail

      • SAMPLE_ALIAS

        public String SAMPLE_ALIAS

      • LIBRARY

        public String LIBRARY
        The name of the library being assayed.

      • REF_BASE

        public char REF_BASE
        The (upper-case) original base on the reference strand.

      • ALT_BASE

        public char ALT_BASE
        The (upper-case) alternative base that is called as a result of DNA damage.

      • CONTEXT

        public String CONTEXT
        The sequence context to which the analysis is constrained.

      • FWD_CXT_REF_BASES

        public long FWD_CXT_REF_BASES
        The number of REF_BASE:REF_BASE alignments at sites with the given reference context.

      • FWD_CXT_ALT_BASES

        public long FWD_CXT_ALT_BASES
        The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.

      • REV_CXT_REF_BASES

        public long REV_CXT_REF_BASES
        The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.

      • REV_CXT_ALT_BASES

        public long REV_CXT_ALT_BASES
        The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.

      • FWD_ERROR_RATE

        public double FWD_ERROR_RATE
        The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).

      • REV_ERROR_RATE

        public double REV_ERROR_RATE
        The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).

      • ERROR_RATE

        public double ERROR_RATE
        The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).

      • QSCORE

        public double QSCORE
        The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).

    • Constructor Detail

      • BaitBiasDetailMetrics

        public BaitBiasDetailMetrics()

    • Method Detail

      • calculateDerivedStatistics

        public void calculateDerivedStatistics()
        Calculate the error rate given the raw counts. Negative rates are set to MIN_ERROR.