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Somatic mutation artifact - unknown mode
In an exome sample in which I'm trying to call somatic mutations, I came across a strange somatic mutation that I cannot interpret and doesn't seem to fit any known error mode that Mutect handles.
The mutation is a T>G (relative to the reference top/+ strand) in 15% of reads (14/92 reads, after PCR duplicate removal). And the mutation is only seen in F2R1 reads. This suggests a single-strand artifact. However, the weird part is this: there is ALSO a strand bias. All 14 of the reads with the mutation are REVERSE strand.
Not only that, but in the 5 out of 14 reads that have the mutation where the forward and reverse reads overlap the mutation, the mutation was only seen in the reverse read. How is that possible? That contradict the possibility of a single-strand artifact.
I've been struggling to understand this and I cannot seem to find an explanation. Any input is appreciated, especially from the Mutect team.