dockstore-tool-samtools-rmdup

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> Options: -s Remove duplicates for single-end reads. By default, the command works for paired-end reads only. -S Treat paired-end reads and single-end reads.

URL(s):

• https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcancercollaboratory%...