picard.analysis.artifacts

Class SequencingArtifactMetrics.BaitBiasSummaryMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics

Enclosing class:

SequencingArtifactMetrics

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 Summary

Fields

Modifier and Type	Field and Description
char	ALT_BASE The (upper-case) alternative base that is called as a result of DNA damage.
java.lang.String	ARTIFACT_NAME A "nickname" of this artifact, if it is a known error mode.
java.lang.String	LIBRARY The name of the library being assayed.
char	REF_BASE The (upper-case) original base on the reference strand.
java.lang.String	SAMPLE_ALIAS The name of the sample being assayed.
double	TOTAL_QSCORE The total Phred-scaled Q-score for this artifact.
java.lang.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.
java.lang.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.
java.lang.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.

Constructor Summary

Constructors

Constructor and Description
BaitBiasSummaryMetrics()

Method Summary

Modifier and Type	Method and Description
void	inferArtifactName() 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 Detail

SAMPLE_ALIAS

public java.lang.String SAMPLE_ALIAS

The name of the sample being assayed.

LIBRARY

public java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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.