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

6       samtools cat - concatenate files together
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SYNOPSIS

9       samtools  cat  [-b list] [-h header.sam] [-o out.bam] in1.bam in2.bam [
10       ... ]
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DESCRIPTION

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

22       -b FOFN Read the list of input BAM or CRAM files from FOFN.  These  are
23               concatenated  prior to any files specified on the command line.
24               Multiple -b FOFN options may be specified to concatenate multi‐
25               ple lists of BAM/CRAM files.
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27       -h FILE Uses  the SAM header from FILE.  By default the header is taken
28               from the first file to be concatenated.
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30       -o FILE Write the concatenated output to FILE.  By default this is sent
31               to stdout.
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33       --no-PG Do not add a @PG line to the header of the output file.
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35       -@, --threads INT
36               Number  of  input/output compression threads to use in addition
37               to main thread [0].
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AUTHOR

41       Written by Heng Li from the Sanger Institute.
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SEE ALSO

45       samtools(1)
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47       Samtools website: <http://www.htslib.org/>
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51samtools-1.13                     7 July 2021                  samtools-cat(1)