Class SequencingArtifactMetrics.PreAdapterSummaryMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
Enclosing class:
SequencingArtifactMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") 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 Summary

    Fields
    Modifier and Type
    Field
    Description
    char
    The (upper-case) alternative base that is called as a result of DNA damage.
    A "nickname" of this artifact, if it is a known error mode.
    The name of the library being assayed.
    char
    The (upper-case) original base on the reference strand.
    The name of the sample being assayed.
    double
    The total Phred-scaled Q-score for this artifact.
    The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
    double
    The Q-score for the worst context.
    The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
    double
    The Q-score for the worst post-context.
    The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
    double
    The Q-score for the worst pre-context.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Label the artifacts corresponding to known error modes.

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
  • Field Details

    • 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 Details

    • PreAdapterSummaryMetrics

      public PreAdapterSummaryMetrics()
  • Method Details

    • inferArtifactName

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