Would it be possible to have a parameter for % mismatch or insertion/deletions instead of a fixed number?
Answer. Yes. ZOOM use the “-mmpct” parameter to denote the percent of mismatches. The “-edpct” parameter and the “-idpct” parameter denote the percent of edit distance and the percent of insertion/deletion length respectively. When using percent parameter on the data set with reads of various length, ZOOM will handle reads of different lenght separately (with Cngrpsv parameter), which is slower than the case a fixed number is assigned where all reads are handled together.
