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MuTect 2 - coverage depth of somatic, germline, and PoN data

robcrobc irelandMember
edited July 2019 in Ask the GATK team
I have a question about MuTect 2 and using data sources at different depths of coverage.

My somatic source is targeted gene panel sequenced to an average of 500x, my germline source is the same targeted panel but sequenced to an average of 100x, and my PoN is 100 individuals whole exome sequenced to an average of 60x.

Is there a risk of skewing the weight of the statistical variant calling model and / or batch effects with the above setup? I'm particulalry concerned with the five-fold difference between the germline and somatic data - or is 100x deep enough for Mutect to be confident with the germline calls?


  • bshifawbshifaw Member, Broadie, Moderator admin
    edited July 2019

    Spoke with the dev team:

    your setup is fine, there should be no issue due to the differing coverages. 100x is quite deep enough for confident germline calling which will be used for filtering with the normal.

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