1samtools-cat(1) Bioinformatics tools samtools-cat(1)
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6 samtools cat - concatenate files together
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9 samtools cat [-b list] [-h header.sam] [-o out.bam] in1.bam in2.bam [
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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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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 multiā
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
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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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41 Written by Heng Li from the Sanger Institute.
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45 samtools(1)
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47 Samtools website: <http://www.htslib.org/>
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51samtools-1.15.1 7 April 2022 samtools-cat(1)