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

# samtools-addreplacerg(1)

adds or replaces read group tags

## NAME

samtools-addreplacerg - adds or replaces read group tags

## SYNOPSIS

samtools addreplacerg \[**-r** *rg-line* \| **-R** *rg-ID*\] \[**-m** *mode*\] \[**-u**\] \[**-o** *out.bam*\] *in.bam*

## DESCRIPTION

Adds or replaces read group tags in a file. Also allows for adding and updating @RG lines in the header.

## OPTIONS

- **-r** *STRING*

  Allows you to specify a read group line to append to the header and applies it to the reads specified by the -m option. If repeated it automatically adds in tabs between invocations.

- **-R** *STRING*

  Allows you to specify the read group ID of an existing @RG line and applies it to the reads specified.

- **-m** *MODE*

  If you choose orphan\_only then existing RG tags are not overwritten, if you choose overwrite\_all, existing RG tags are overwritten. The default is overwrite\_all.

- **-o** *STRING*

  Write the final output to STRING. The default is to write to stdout.

  By default, samtools tries to select a format based on the output filename extension; if output is to standard output or no format can be deduced, **sam** is selected.

- **-u**

  Output uncompressed SAM, BAM or CRAM.

- **-w**

  Overwrite an existing @RG line, if a new one with the same ID value is provided.

- **--no-PG**

  Do not add a @PG line to the header of the output file.

- **-@, --threads** *INT*

  Number of input/output compression threads to use in addition to main thread \[0\].

## AUTHOR

Written by Martin Pollard from the Sanger Institute.

## SEE ALSO

[*samtools*(1)](/samtools/1.md), [*samtools-split*(1)](/samtools-split/1.md)

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