TargetMetrics

Metrics

Category Metrics

Overview

TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA). TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics.

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

Metric	Summary
PROBE_SET	The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
PROBE_TERRITORY	The number of unique bases covered by the intervals of all probes in the probe set
ON_PROBE_BASES	The number of PF aligned probed bases that mapped to a baited region of the genome.
NEAR_PROBE_BASES	The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.
OFF_PROBE_BASES	The number of PF aligned bases that mapped to neither on or near a probe.
PCT_SELECTED_BASES	The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
PCT_OFF_PROBE	The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
ON_PROBE_VS_SELECTED	The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
MEAN_PROBE_COVERAGE	The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
FOLD_ENRICHMENT	The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.