Package picard.analysis.artifacts
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
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
-
Field Details
-
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.
-
-
Constructor Details
-
PreAdapterSummaryMetrics
public PreAdapterSummaryMetrics()
-
-
Method Details
-
inferArtifactName
public void inferArtifactName()Label the artifacts corresponding to known error modes.
-