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/>