---
name: "samtools-rmdup"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samtools-rmdup"
---

# samtools-rmdup(1)

removes duplicate reads (obsolete)

## 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**This command is obsolete.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 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).

## 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/1.md)

Samtools website: \<http://www.htslib.org/\>