> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/access-quality-control-v2/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/access-quality-control-v2/add-qc-workflow/introduction/capture-metrics.md).

# Capture metrics

Validating the efficacy of the Pool A and Pool B bait sets.

## Introduction

There are several sections displaying bait set capture efficiency. Each section corresponds to a separate BAM type and bait set combination. The tool used to produce the metrics is GATK-CollectHsMetrics. By default, only the mean bait coverage, mean target coverage, and % Usable bases on-target are displayed. However, there are many more metrics that can be toggled to display by clicking on the `Configure Columns` button.

![Example MultiQC report showing insert size distribution for 20 samples (10 plasma and 10 buffy coat samples).](https://307995240-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MbqIfOAQqfG2kMfi2uM%2Fsync%2Fbd1cbaa0dad3d23a897e519764a167e364835852.png?generation=1624554771157328\&alt=media)

## Methods

**Tool used:** [GATK-CollectHsMetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard-)\
 **BAM type:** (1) Uncollapsed BAM, (1) Collapsed BAM, (1) Duplex BAM, and (4) Simplex BAM\
 **Regions:** Pool A and Pool B

## Interpretation

The aim is to have high coverage across Pool A and Pool B panels.