bbmap, mapq and uniquelly mapped reads filtering

1

Hi,

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.

  1. Does for bbmap similar correspondence exists?
  2. If yes, what mapq threshold should be used to get only unique mappings?
  3. Is there any general method (no matter what aligner was used) to get only uniquelly mapped reads from sam file, for example using flags and samtools?


alignment


mapq

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