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) |
GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.
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