'\" t
.TH samtools-addreplacerg 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools-addreplacerg \- adds or replaces read group tags
.\"
.\" Copyright (C) 2008-2011, 2013-2018, 2020 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
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.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
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.SH SYNOPSIS
.PP
samtools addreplacerg
.RB [ -r
.I rg-line
|
.B -R
.IR rg-ID ]
.RB [ -m
.IR mode ]
.RB [ -u ]
.RB [ -o
.IR out.bam ]
.I in.bam

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

.SH OPTIONS
.TP 8
.BI "-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.
.TP 8
.BI "-R " STRING
Allows you to specify the read group ID of an existing @RG line and applies it
to the reads specified.
.TP 8
.BI "-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.
.TP 8
.BI "-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,
.B sam
is selected.
.TP 8
.B -u
Output uncompressed SAM, BAM or CRAM.
.TP 8
.B -w
Overwrite an existing @RG line, if a new one with the same ID value is provided.
.TP 8
.BI --no-PG
Do not add a @PG line to the header of the output file.
.TP 8
.BI "-@, --threads " INT
Number of input/output compression threads to use in addition to main thread [0].

.SH AUTHOR
.PP
Written by Martin Pollard from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1),
.IR samtools-split (1)
.PP
Samtools website: <http://www.htslib.org/>