in overlap position, gencore doesn't reset quality #48
Description
hi ,
in the document : In the overlapped region, if a base and its pair are mismatched, its quality score will be adjusted to: max(0, this_qual - pair_qual), but i find the quality score doesn't reset,
the 134G8 means G>T in the first read, and the second read is still G, the quality of this position are both D(Q35), so G>T mutation is called by vardict since the quality seems good.