FORUMCategory: BioinformaticsHow to get coverage from a bam file?
jrosner Staff asked 2 years ago



I have a set of bam files for which I need to calculate coverage as a whole and also over specific regions.  What would be the method to do this? Or better yet is there a software tool that will do this for me?

1 Answers
zhibin Staff answered 2 years ago



Usually, I run bamqc in QualiMap (http://qualimap.bioinfo.cipf.es/) after I generate bam files. The tool gives you not only the coverage but all sorts of QC of your bam file.