samtools addreplacerg [-r rg-line | -R rg-ID] [-m mode] [-l level] [-o out.bam] in.bam
Adds or replaces read group tags in a file.
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.
Allows you to specify the read group ID of an existing @RG line and applies it to the reads specified.
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.
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.
Do not add a @PG line to the header of the output file.
Number of input/output compression threads to use in addition to main thread .
Written by Martin Pollard from the Sanger Institute.
Samtools website: <http://www.htslib.org/>
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