Manual page from samtools-1.19
released on 12 December 2023


samtools addreplacerg – adds or replaces read group tags


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


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



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.


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


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.


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.


Output uncompressed SAM, BAM or CRAM.


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


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].


Written by Martin Pollard from the Sanger Institute.


samtools (1), samtools-split (1)

Samtools website: <>