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
samtools rmdup [-sS] <input.srt.bam> <out.bam>
Remove duplicates for single-end reads. By default, the command works for paired-end reads only.
Treat paired-end reads and single-end reads.