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samtools-cat(1)		     Bioinformatics tools	       samtools-cat(1)

NAME
       samtools	cat - concatenate files	together

SYNOPSIS
       samtools	 cat  [-b list]	[-h header.sam]	[-o out.bam] in1.bam in2.bam [
       ... ]

DESCRIPTION
       Concatenate BAMs	or CRAMs. Although this	works on either	BAM  or	 CRAM,
       all  input  files  must	be the same format as each other. The sequence
       dictionary of each input	file must be identical,	although this  command
       does  not  check	 this.	This  command uses a similar trick to reheader
       which enables fast BAM concatenation.

OPTIONS
       -b FOFN Read the	list of	input BAM or CRAM files	from FOFN.  These  are
	       concatenated  prior to any files	specified on the command line.
	       Multiple	-b FOFN	options	may be specified to concatenate	multi-
	       ple lists of BAM/CRAM files.

       -h FILE Uses  the SAM header from FILE.	By default the header is taken
	       from the	first file to be concatenated.

       -o FILE Write the concatenated output to	FILE.  By default this is sent
	       to stdout.

       --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 Heng Li from the Sanger Institute.

SEE ALSO
       samtools(1)

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

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

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

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