Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads).
Usage: samtools rmdup [-sS] <input.srt.bam> <out.bam>
-s Remove duplicates for single-end reads. By default, the command works for p
This is a companion discussion topic for the original entry at quay.io/cancercollaboratory/dockstore-tool-samtools-rmdup