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BAMCAT(1) General Commands Manual BAMCAT(1)


bamcat - concatenate BAM files


bamcat [options]


bamcat reads a set of input BAM files, merges the headers, concatenates the alignment data and writes the output on standard output in BAM format. The input files can be specified via the I key. Any none key=value arguments given after the key=value pairs will also be considered as input files.

The following key=value pairs can be given:

I=<stdin>: name of the input file. This key can be used multiple times

level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are

zlib/gzip default compression level
zlib/gzip level 1 (fast) compression
zlib/gzip level 9 (best) compression

If libmaus has been compiled with support for igzip (see then an additional valid value is

igzip compression

verbose=<1>: Valid values are

print progress report on standard error
do not print progress report

tmpfile=<filename>: prefix for temporary files. By default the temporary files are created in the current directory

md5=<0|1>: md5 checksum creation for output file. Valid values are

do not compute checksum. This is the default.
compute checksum. If the md5filename key is set, then the checksum is written to the given file. If md5filename is unset, then no checksum will be computed.

md5filename file name for md5 checksum if md5=1.

index=<0|1>: compute BAM index for output file. Valid values are

do not compute BAM index. This is the default.
compute BAM index. If the indexfilename key is set, then the BAM index is written to the given file. If indexfilename is unset, then no BAM index will be computed.

indexfilename file name for BAM index if index=1.

streaming=<0>: streaming mode inactive or active. By default streaming mode is inactive. Valid values are

streaming mode is inactive. Only one input file will be opened at any single time, but each input file is openend twice (once for reading the header only, the second time for extracting the alignment data).
streaming mode is active. All input files will be opened at the same time and kept open until data processing is finished. Each input file will be opened only once.


Written by German Tischler.


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Copyright © 2009-2013 German Tischler, © 2011-2013 Genome Research Limited. License GPLv3+: GNU GPL version 3 <>
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

October 2013 BIOBAMBAM