Package picard.analysis.artifacts
Class SequencingArtifactMetrics.BaitBiasSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
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- 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.
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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
ARTIFACT_NAME
A "nickname" of this artifact, if it is a known error mode.String
LIBRARY
The name of the library being assayed.char
REF_BASE
The (upper-case) original base on the reference strand.String
SAMPLE_ALIAS
The name of the sample being assayed.double
TOTAL_QSCORE
The total Phred-scaled Q-score for this artifact.String
WORST_CXT
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.double
WORST_CXT_QSCORE
The Q-score for the worst context.String
WORST_POST_CXT
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.double
WORST_POST_CXT_QSCORE
The Q-score for the worst post-context.String
WORST_PRE_CXT
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.double
WORST_PRE_CXT_QSCORE
The Q-score for the worst pre-context.
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Constructor Summary
Constructors Constructor Description BaitBiasSummaryMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
inferArtifactName()
Label the artifacts corresponding to known error modes.
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Field Detail
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
The name of the sample being assayed.
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LIBRARY
public String LIBRARY
The name of the library being assayed.
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REF_BASE
public char REF_BASE
The (upper-case) original base on the reference strand.
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ALT_BASE
public char ALT_BASE
The (upper-case) alternative base that is called as a result of DNA damage.
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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.
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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.
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WORST_CXT_QSCORE
public double WORST_CXT_QSCORE
The Q-score for the worst context.
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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.
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WORST_PRE_CXT_QSCORE
public double WORST_PRE_CXT_QSCORE
The Q-score for the worst pre-context.
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WORST_POST_CXT
public String WORST_POST_CXT
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
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WORST_POST_CXT_QSCORE
public double WORST_POST_CXT_QSCORE
The Q-score for the worst post-context.
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ARTIFACT_NAME
public String ARTIFACT_NAME
A "nickname" of this artifact, if it is a known error mode.
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