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samtools-rmdup(1) Bioinformatics tools samtools-rmdup(1) NAME samtools rmdup - removes duplicate reads (obsolete) SYNOPSIS samtools rmdup [-sS] input.srt.bam out.bam DESCRIPTION This command is obsolete. Use markdup instead. Remove potential PCR duplicates: if multiple read pairs have identical ex- ternal coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and re- quires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads). 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. LIMITATIONS o Samtools paired-end rmdup does not work for unpaired reads (e.g. orphan reads or ends mapped to different chromosomes). If this is a concern, please use Picard's MarkDuplicates which correctly handles these cases, although a little slower. AUTHOR Written by Heng Li from the Sanger Institute. SEE ALSO samtools(1) Samtools website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-rmdup(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | LIMITATIONS | AUTHOR | SEE ALSO
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