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

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

-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].

Written by Martin Pollard from the Sanger Institute.