bam-qc-metrics

Quality control metrics for BAM alignment files.

Process a BAM file and write metrics and metadata in JSON format.

Prerequisites

The bedtools executable must be available on the current PATH. Note that version 2.28.0 of the statically compiled binary on Github has an inconsistent version number, which means it does not work with pybedtools. Instead it is necessary to download the tarball and compile the bedtools binary locally.

Usage

There are two command-line scripts:

• bin/run_bam_qc.py to run all metrics
• bin/write_fast_metrics.py to run a faster subset of metrics, eg. for RNASeqQC

Run either script with --help for instructions.

Tests

Run test/test.py for Python tests.

Release procedure

Before a release, the package version number in ./etc/versions/bam_qc_metrics/VERSION must be updated.

The package version number also appears in JSON test output, and must be updated prior to a new release. The script bin/update_test_data_version.py is awaiting a bug fix; for details and a workaround, see the issue on Github.

Metric notes

See metrics.md for a detailed account of the metrics in use.

Conventions

• Changelog: See CHANGELOG.md and https://keepachangelog.com/en/1.0.0/
• Semantic Versioning: See https://semver.org/