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 multiple
               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-1.19.2                                  24 January 2024                                 samtools-cat(1)