Man page - samtools-addreplacerg(1)

Packages contains this manual

Package:  samtools
apt-get install samtools

Manuals in package:
• samtools-head(1)
• samtools-reference(1)
• samtools-addreplacerg(1)
• samtools(1)
• samtools-collate(1)
• samtools-fixmate(1)
• samtools-cat(1)
• samtools-markdup(1)
• samtools-targetcut(1)
• samtools-tview(1)
• wgsim(1)
• samtools-samples(1)
• samtools-split(1)
• samtools-sort(1)
• samtools-index(1)
• samtools-coverage(1)
• samtools-dict(1)
• samtools-import(1)
• samtools-cram-size(1)
• ace2sam(1)
• samtools-bedcov(1)
• samtools-flagstat(1)
• samtools-reheader(1)
• samtools-depth(1)
• samtools-flags(1)
• samtools-phase(1)
• samtools-view(1)
• samtools-merge(1)
• samtools-rmdup(1)
• samtools-fqidx(1)
• samtools-fasta(1)
• samtools-fastq(1)
• samtools-quickcheck(1)
• samtools-calmd(1)
• samtools-mpileup(1)
• samtools.pl(1)
• samtools-consensus(1)
• samtools-depad(1)
• samtools-ampliconstats(1)
• samtools-faidx(1)
• samtools-ampliconclip(1)
• samtools-reset(1)
• samtools-idxstats(1)
• samtools-stats(1)
Documentations in package:
• samtools

Manual

samtools-addreplacerg

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO

---

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.

-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.

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

---