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Mutect2 - Ploidy setting also for normals?

AkGoepfertAkGoepfert BelgienMember


I have a question regarding the ploidy setting of the mutect2.

I have two whole-exome sequencing datasets of a tumor sample – both treated under different conditions. The goal is to find genetic differences (SNVs and indels) between those two samples. One is being called the "normal" and the other the so-called "tumor" sample.

Because I am using the same tumor sample, both (tumor and normal) have a ploidy of 4.

The question is, if the ploidy setting is only taking account for the tumor sample? And if so, if there is a setting which also changes the ploidy setting of the normal sample? Or is the "normal" sample not by default diploid?

How can I deal with this in a proper way?

Thanks a lot for your help!


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @AkGoepfert,

    You don't need to set ploidy when calling somatic variants -- in fact that setting would be ignored. Somatic variation is modeled differently. I'm not entirely sure what is the right way to deal with your situation -- I think it would be preferable to compare both tumor samples independently to a real normal sample.

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