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 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, 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-1.19.2                                  24 January 2024                        samtools-addreplacerg(1)