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samtools-addreplacerg(1) Bioinformatics tools samtools-addreplacerg(1) 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 up- dating @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 overwrit- ten, 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 std- out. 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-split(1) Samtools website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-addreplacerg(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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