BamQC
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.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of bamqc and load default version of bamqc as
module avail bamqc/ # list available modules module load bamqc # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail bamqc
and choose explicit version you want to use.
Documentation
https://github.com/s-andrews/BamQC and bamqc -h