BaitBiasSummaryMetrics

Metrics

Category Metrics

Overview

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.

This table summarizes the values that are specific to this metric.

Metric	Summary
SAMPLE_ALIAS	The name of the sample being assayed.
LIBRARY	The name of the library being assayed.
REF_BASE	The (upper-case) original base on the reference strand.
ALT_BASE	The (upper-case) alternative base that is called as a result of DNA damage.
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	The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT_QSCORE	The 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	The 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	The 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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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.