<p>Hi there.</p>

<p>I have two bam files which followed the preprocessing including GATK.</p>

<p>and I would like to check these two bam files read quality as graph in order to understand easily.</p>

<p>Is any library or program that provides the read quality of these bam files containing with some charts?</p>

RSeqQC might help you to get mapping statistics

    bam_stat.py -i myFile.bam

for stats in graphical way

qualimap is nice one, you can find it [here][1] PS: I have never used it.

for other information this site would be useful for you

http://barcwiki.wi.mit.edu/wiki/SOPs/miningSAMBAM

 [1]: http://qualimap.bioinfo.cipf.es/