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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

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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