1samtools-addreplacerg(1)     Bioinformatics tools     samtools-addreplacerg(1)
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NAME

6       samtools addreplacerg - adds or replaces read group tags
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SYNOPSIS

9       samtools  addreplacerg  [-r  rg-line  |  -R  rg-ID]  [-m mode] [-u] [-o
10       out.bam] in.bam
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DESCRIPTION

14       Adds or replaces read group tags in a file. Also allows for adding  and
15       updating @RG lines in the header.
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OPTIONS

19       -r STRING
20               Allows you to specify a read group line to append to the header
21               and applies it to the reads specified by the -m option. If  re‐
22               peated it automatically adds in tabs between invocations.
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24       -R STRING
25               Allows you to specify the read group ID of an existing @RG line
26               and applies it to the reads specified.
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28       -m MODE If you choose orphan_only then existing RG tags are  not  over‐
29               written,  if  you  choose  overwrite_all,  existing RG tags are
30               overwritten. The default is overwrite_all.
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32       -o STRING
33               Write the final output to STRING. The default is  to  write  to
34               stdout.
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36               By default, samtools tries to select a format based on the out‐
37               put filename extension; if output is to standard output  or  no
38               format can be deduced, sam is selected.
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40       -u      Output uncompressed SAM, BAM or CRAM.
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42       -w      Overwrite  an  existing @RG line, if a new one with the same ID
43               value is provided.
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45       --no-PG Do not add a @PG line to the header of the output file.
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47       -@, --threads INT
48               Number of input/output compression threads to use  in  addition
49               to main thread [0].
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AUTHOR

53       Written by Martin Pollard from the Sanger Institute.
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SEE ALSO

57       samtools(1), samtools-split(1)
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59       Samtools website: <http://www.htslib.org/>
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63samtools-1.13                     7 July 2021         samtools-addreplacerg(1)
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