I'm looking for a way to apply a %id + %'length of query aligned' cutoff to the alignments in a sam file. I want to filter the long, local alignments of bwa mem using constraints like "show me only hits matching at 90% identity with at least 75% of the query length aligning to the reference".
I can imagine how this would be done from the sam files, using callmd to look at the alignments in detail, but I am hoping someone has a tool already built that can do this. I'm also really missing the alignment chains that old wu-blast could construct, that would give a clearer view for this kind of cutoff across the entire alignment which (in blast terms) could span multiple HSPs (I guess in bwa mem terms that would be multiple MEMs?). But I will settle for a tool that can just apply this cutoff to each individual alignment line in a sam file.
Does such a tool already exist?
I can imagine how this would be done from the sam files, using callmd to look at the alignments in detail, but I am hoping someone has a tool already built that can do this. I'm also really missing the alignment chains that old wu-blast could construct, that would give a clearer view for this kind of cutoff across the entire alignment which (in blast terms) could span multiple HSPs (I guess in bwa mem terms that would be multiple MEMs?). But I will settle for a tool that can just apply this cutoff to each individual alignment line in a sam file.
Does such a tool already exist?