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.
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-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.
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-u |
Output uncompressed SAM, BAM or CRAM. | ||
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-w |
Overwrite an existing @RG line, if a new one with the same ID value is provided. | ||
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--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/>;