bamutils / keepbest

Parses BAM file and keeps the best mapping for reads that have multiple
mappings. If an aligner outputs multiple mappings for each read, this will
remove mappings, keeping only the best one.

Usage: bamutils keepbest {-tag tag} infile.bam outfile.bam

   -tag tag    Use {tag} to determine which mappings to keep. This can be any
               tag present in the BAM file or "MAPQ" (default: AS).