I'd like to know, how do postalignment filtering to get only uniquelly mapped reads.
I know that it is possible at the
bbmap level, i.e. during mapping.
I've read, that for aligners like
BWA there are correspondence between
mapq value and uniqueness of alignment.
- Does for
bbmapsimilar correspondence exists?
- If yes, what mapq threshold should be used to get only unique mappings?
- Is there any general method (no matter what aligner was used) to get only uniquelly mapped reads from
samfile, for example using flags and