Class SequencingArtifactMetrics.BaitBiasSummaryMetrics

  • Enclosing class:
    SequencingArtifactMetrics

    @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public static class SequencingArtifactMetrics.BaitBiasSummaryMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Summary analysis of a single bait bias artifact, also known as a reference bias artifact. These artifacts occur during or after the target selection step, and correlate with substitution rates that are "biased", or higher for sites having one base on the reference/positive strand relative to sites having the complementary base on that strand. For example, a G>T artifact during the target selection step might result in a higher G>T / C>A substitution rate at sites with a G on the positive strand (and C on the negative), relative to sites with the flip (C positive / G negative). This is known as the "G-Ref" artifact.
    • Field Detail

      • SAMPLE_ALIAS

        public String SAMPLE_ALIAS
        The name of the sample being assayed.
      • 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.
      • TOTAL_QSCORE

        public double TOTAL_QSCORE
        The total Phred-scaled Q-score for this artifact. A lower Q-score means a higher probability that a REF_BASE:ALT_BASE observation randomly picked from the data will be due to this artifact, rather than a true variant.
      • WORST_CXT

        public String WORST_CXT
        The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
      • WORST_CXT_QSCORE

        public double WORST_CXT_QSCORE
        The Q-score for the worst context.
      • WORST_PRE_CXT

        public String WORST_PRE_CXT
        The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
      • WORST_PRE_CXT_QSCORE

        public double WORST_PRE_CXT_QSCORE
        The Q-score for the worst pre-context.
      • WORST_POST_CXT

        public String WORST_POST_CXT
        The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
      • WORST_POST_CXT_QSCORE

        public double WORST_POST_CXT_QSCORE
        The Q-score for the worst post-context.
      • ARTIFACT_NAME

        public String ARTIFACT_NAME
        A "nickname" of this artifact, if it is a known error mode.
    • Constructor Detail

      • BaitBiasSummaryMetrics

        public BaitBiasSummaryMetrics()
    • Method Detail

      • inferArtifactName

        public void inferArtifactName()
        Label the artifacts corresponding to known error modes.