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samtools-split(1)	     Bioinformatics tools	     samtools-split(1)

NAME
       samtools	split -	splits a file by read group.

SYNOPSIS
       samtools	split [options]	merged.sam|merged.bam|merged.cram

DESCRIPTION
       Splits  a file by read group, producing one or more output files	match-
       ing a common prefix (by default based on	the input filename) each  con-
       taining one read-group.

       The  -u	option	may  be	 used  to  specify the output filename for any
       records without an RG tag.

OPTIONS
       -u FILE1	     Put reads with no RG tag or an unrecognised RG  tag  into
		     FILE1

       -h FILE2	     Use  the header from FILE2	when writing the file given in
		     the -u option.  This header completely replaces  the  one
		     from  the input file.  It must be compatible with the in-
		     put file header, which means it must have the same	number
		     of	 references listed in the @SQ lines and	the references
		     must be in	the same order and have	the same lengths.

       -f STRING     Output filename format string (see	below) ["%*_%#.%."]

       -v	     Verbose output

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

       Format string expansions:

			%%   %
			%*   basename
			%#   @RG index
			%!   @RG ID
			%.   output format filename extension

AUTHOR
       Written by Martin Pollard from the Sanger Institute.

SEE ALSO
       samtools(1), samtools-addreplacerg(1)

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

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

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

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