Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
samtools-addreplacerg(1)     Bioinformatics tools     samtools-addreplacerg(1)

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.

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 re-
	       peated 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 over-
	       written,	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 out-
	       put  filename  extension; if output is to standard output or no
	       format can be deduced, sam is selected.

       -u      Output uncompressed SAM,	BAM or CRAM.

       --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/>

samtools-1.11		       22 September 2020      samtools-addreplacerg(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=samtools-addreplacerg&sektion=1&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help