bamutils / best

Given a BAM file sorted by read name with potentially multiple mappings, this
will remove all but the best mapping.

The value of the attribute/tag given will be used to determine which reads
should be kept and which should be discarded. The tag should be a numeric
(int/float) type. Multiple tags may be used. This defaults to 'AS+, NM-'.

Usage: bamutils best {opts} input.bam output.bam

  -tag VAL    Tag to use to determine from which file reads will be taken.
              (must be type :i or :f) You may have more than one of these,
              in which case they will be sorted in order. You can add a +/-
              at the end of the name to signify sort order (asc/desc). 
              [default: AS+, NM-]

  -fail filename.bam    Write all failed mappings to this file.