Package picard.analysis.artifacts
Class SequencingArtifactMetrics.BaitBiasSummaryMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.artifacts.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.
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Field Summary
FieldsModifier and TypeFieldDescriptionchar
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
Label the artifacts corresponding to known error modes.Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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SAMPLE_ALIAS
The name of the sample being assayed. -
LIBRARY
The name of the library being assayed. -
REF_BASE
public char REF_BASEThe (upper-case) original base on the reference strand. -
ALT_BASE
public char ALT_BASEThe (upper-case) alternative base that is called as a result of DNA damage. -
TOTAL_QSCORE
public double TOTAL_QSCOREThe 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
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_QSCOREThe Q-score for the worst context. -
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_QSCOREThe Q-score for the worst pre-context. -
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_QSCOREThe Q-score for the worst post-context. -
ARTIFACT_NAME
A "nickname" of this artifact, if it is a known error mode.
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Constructor Details
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BaitBiasSummaryMetrics
public BaitBiasSummaryMetrics()
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Method Details
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inferArtifactName
public void inferArtifactName()Label the artifacts corresponding to known error modes.
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