Manual page from samtools-1.10
released on 6 December 2019

NAME

samtools addreplacerg – adds or replaces read group tags

SYNOPSIS

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

DESCRIPTION

Adds or replaces read group tags in a file.

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, bam is selected.

--no-PG

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

AUTHOR

Written by Martin Pollard from the Sanger Institute.

SEE ALSO

samtools (1), samtools-split (1)

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