Test-drive the GATK tools and Best Practices pipelines on Terra
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How does MuTect2 treat heterozygous mutant to homozygous mutant?
I found in one case of my samples that, the matched normal is a heterozygous mutant, e.g. the reference is C, the matched normal is 60% C and 40% G. While the tumor is 20%C and 81% G (% in terms of number of reads). This suggests it could be a heterzygous mutant in normal and becomes almost homozygous mutant in tumor. Of course, other explanations also exist, such as sample contamination.
This mutant is discovered by VarScan, but not MuTect2.
I am wondering whether MuTect2 discard any locus which is not pure enough in the normal, e.g. 60% same as reference. Or is there a way we could set a filter asking MuTect2 to reserve such het-to-homo mutation?
There are over 80 reads for any allele in this case. Many thanks!