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MuTect2 to compare 2 tumor samples

I have capture data of 2 tumor biopsies from 1 patient, and would like to compare the two for mutational similarities and differences. I don't have a normal control.
I tested if MuTect2 ( could help me in my analysis by comparing the 2, with one of the tumor samples as "normal" and the other as "tumor". Analysis results gave me a nice list of variants that are not present in one tumor but present in the other, however i'm missing the variants that are overlapping (but differ in vaf levels, for example 20% in one tumor and 80% in the other).
Is there a way to tweak MuTect2 in such a way that also the overlapping variants (that are now obviously regarded as 'germline') are outputted?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    The team lead just said he would work on allowing Mutect2 to output germline sites as well as somatic sites. That should be a new feature soon.

    In the meantime, you may consider running Mutect2 in tumor-only mode on both of your samples and using SelectVariants with `--concordance.

    Also, you may find this post helpful. Although it illustrates the opposite of what you want, you may find some helpful tips in there.


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