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Mutect2 - Ploidy setting also for normals?
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!