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/>