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MuTectv2 BQ

Johanna_SgJohanna_Sg SwedenMember


I am wondering about getting the (average) base quality value for the variants called by MuTect2, There were such a column for MuTect v1 output, but not for for MuTect v2?

Best Answer


  • Johanna_SgJohanna_Sg SwedenMember

    Thank you for your rapid reply, I do not think however that the LOD-scores reflect so well the base quality for that variant, we have samples with variants called by Mutect2 with very low base quality (according to results from MuTect1), around 13-19 and the TLOD can be from 6,3 to at least 40.. I migth want to be able to remove (filter post run) variants that have such low BQ but now my only option is to rerun with a higher treshhold for MBQ? default is 10 (why so low?). Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Actually I was wrong, that information is still output but in a different form. Have a look at: the QSS annotation.

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