Class SequencingArtifactMetrics.PreAdapterSummaryMetrics

  • Enclosing class:
    SequencingArtifactMetrics

    public static class SequencingArtifactMetrics.PreAdapterSummaryMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Summary analysis of a single pre-adapter artifact. These artifacts occur on the original template strand, before the addition of adapters, so they correlate with read number / orientation in a specific way. For example, the well-known "Oxo-G" artifact occurs when a G on the template strand is oxidized, giving it an affinity for binding to A rather than the usual C. Thus PCR will introduce apparent G>T substitutions in read 1 and C>A in read 2. In the resulting alignments, a given G>T or C>A observation could either be: 1. a true mutation 2. an OxoG artifact 3. some other kind of artifact On average, we assume that 1 and 3 will not display this read number / orientation bias, so their contributions will cancel out in the calculation.
    • 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

      • PreAdapterSummaryMetrics

        public PreAdapterSummaryMetrics()
    • Method Detail

      • inferArtifactName

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