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Depthofcoverage Query

I would like to get the average coverage of all the captured bases in a bam file. What would be the best way to do this? What I am looking is a simple one number like 40X. Given that there may be millions of bases sequenced in a next gen study I would like to get the overall average coverage for all these bases as a single number.
i have used DepthOfcoverage module but i am not getting average coverage its giving coverage for each base
note: My bam file is only for one gene not for whole genome.
Please let me know


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Meenu,

    If you run DepthOfCoverage with a list of intervals corresponding to the region(s) you are interested in, it will give you a summary of coverage per interval, which I think is what you are looking for.

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