BamQC

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Description

BamQC is an application which takes a BAM file containing mapped data and runs a series of tests on it to generate a comprehensive QC report. This will help you to understand your data and will tell you if there is anything unusual the files you have analysed. Each test is flagged as a pass, warning or fail depending on how far it departs from what you'd expect from a normal large data set with no significant biases.

It's important to stress that warnings or even failures do not necessarily mean that there is a problem with your data, only that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.

Availability

There is no official stable release. The module contains Git snapshot 4b3d20f (version 0.1.25_devel)

 bamqc

Use

 module add bamqc
 bamqc -h
 bamqc file.bam

Documentation

https://github.com/s-andrews/BamQC and bamqc -h

Licence

GNU GPL v3

Program administrator

meta@cesnet.cz

Homepage

URL: https://github.com/s-andrews/BamQC