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MuTect2 high insertion counts?
I am using Mutect2 to analyze blood vs. FFPE tumor samples (breast cancer).
I am getting (what I think are) unusually high insertion:SNV ratios - the ratio is between 2:1 and 3:1, thus high numbers of insertions.
The deletion:SNV ratio is between 0.1:1 and 0.25:1.
I was wondering if anyone else had experienced something similar or had any advice / comments?