focal (1) samtools-addreplacerg.1.gz

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/>