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/>