Hello BioStars,

Is there a tool which generates mapping quality score distributions from bam files?

I know I could potentially do this myself, but I am looking for something which would essentially do the work for me, and also something which plugs in nicely to multiqc

I have had a quick search, and it is surprisingly difficult to find a tool which provides this functionality, so I am just wondering if I am missing something obvious here? The obvious candidate would be something like picard, but picard does not seem to offer this functionality from what I can tell

Thanks in advance!
I'm pretty sure that [Qualimap BamQC][1] (not to be confused with the BamQC tool from Babraham mentioned above) calculates and plots this. Qualimap is supported by MultiQC, however off the top of my head, I don't think that MultiQC replicates this plot in reports. I doubt it would be particularly difficult to add if you fancy it (or opening a GitHub issue with some example data), or you could probably sidestep that by using MultiQC's "[custom content][2]" feature.


  [1]: http://qualimap.conesalab.org/doc_html/analysis.html
  [2]: https://multiqc.info/docs/#custom-content