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

FreeBSD Manual Pages

  
 
  

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

NAME
       samtools	reheader - replaces the	header in the input file

SYNOPSIS
       samtools	reheader [-iP] [-c CMD | in.header.sam ] in.bam

DESCRIPTION
       Replace	the  header  in	in.bam with the	header in in.header.sam.  This
       command is much faster than replacing the header	with  a	 BAM->SAM->BAM
       conversion.

       By default this command outputs the BAM or CRAM file to standard	output
       (stdout), but for CRAM format files it has the option to	perform	an in-
       place  edit,  both  reading  and	writing	to the same file.  No validity
       checking	is performed on	the header, nor	that it	 is  suitable  to  use
       with the	sequence data itself.

OPTIONS
       -P, --no-PG
	       Do not add a @PG	line to	the header of the output file.

       -i, --in-place
	       Perform the header edit in-place, if possible.  This only works
	       on CRAM files and only if there is sufficient room to store the
	       new header.  The	amount of space	available will differ for each
	       CRAM file.

       -c, --command CMD
	       Allow the header	from in.bam to be processed  by	 external  CMD
	       and  read back the result. When used in this manner, the	exter-
	       nal header file in.header.sam has to be omitted.

	       CMD must	take the original header through stdin in  SAM	format
	       and output the modified header to stdout.  CMD is passed	to the
	       system's	command	shell.	Care should be	taken  to  ensure  the
	       command	is quoted correctly to avoid unwanted shell expansions
	       (for example of $ variables).

	       CMD must	return an exit status of zero.

EXAMPLES
       o Remove	comment	lines

	   samtools reheader -c	'grep -v ^@CO' in.bam

       o Add "Chr" prefix to chromosome	names.	Note extra backslashes	before
	 dollar	signs to prevent unwanted shell	variable expansion.

	   samtools reheader -c	'perl -pe "s/^(@SQ.*)(\tSN:)(\d+|X|Y|MT)(\s|\$)/\$1Chr\$2\$3/"'	in.bam

       o Remove	"Chr" prefix

	   samtools reheader -c	'perl -pe "s/^(@SQ.*)(\tSN:)Chr/\$1\$2/"' in.bam

AUTHOR
       Written	by  Heng  Li  with modifications by James Bonfield and Valeriu
       Ohan, all from the Sanger Institute.

SEE ALSO
       samtools(1)

       Samtools	website: <http://www.htslib.org/>

samtools-1.10			6 December 2019		  samtools-reheader(1)

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

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=samtools-reheader&sektion=1&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help