Background: I was triaging a particular passing variant call from Mutect2 (there was no evidence for this variant in the original BAMs), so I ran Mutect2 again producing the bamout.
Top panel = Artifical Haplotypes; Bottom panel = Tumor alignments (from bamout)
It seems there is a pretty noisy re-alignment going on; however, what I'm more confused about is: shouldn't the tumor alignments in the bamout reflect the realignments that occurred in Mutect2? I was hoping to see why all of these variants were showing up when my input reads were looking pretty clean overall.
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