Open ctsa opened 9 years ago
Additionally, I believe this gives you control over filtering PR, exposing a flag to filter over SR would be nice too.
Related, I have found sometimes with these spurious mappings is one side of the PR maps with high mapq, but the other side maps with a low one (not sure how the --min-mapq flag operates if it keeps the pair if one satisfies or requires both to satisfy). Similar comments regarding the AS score vs. MAPQ, but not sure if the algorithm accounts for --min-alignment-score internally.
via @hguturu