samtools-addreplacerg1
Adds or replaces read group tags
Usage
samtools addreplacerg
[{-r
rg-line | -R
rg-ID}]
[-m
mode]
[-u]
[-o
out.bam]
in.bam
Overview
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,
samis 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].
Releases
3 releases since Debian 11 (Bullseye); the text changed 2 times.
-w since Debian 12 (Bookworm).