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.
There is no official stable release. The module contains Git snapshot
4b3d20f (version 0.1.25_devel)
module add bamqc bamqc -h bamqc file.bam