samtools-cat - concatenate files together
samtools cat [
-b list] [
-h header.sam] [
-o
out.bam]
in1.bam in2.bam [ ... ]
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.
-
-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].
Written by Heng Li from the Sanger Institute.
samtools(1)
Samtools website: <
http://www.htslib.org/>