bamsplit - split BAM files

       Written by German Tischler.

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

BIOBAMBAM                                         October 2013                                       BAMSPLIT(1)

       bamsplit  reads  a  BAM  file  via  standard input and creates a set of output files with at most a given
       number of alignments each. The concatenation of the output files via  bamcat  restores  the  sequence  of
       alignments in the original input file. The splitting does not consider read pairs, i.e. the ends of pairs
       can end up in separate files.

       The following key=value pairs can be given:

       n=<65536>: number of alignments per output file.

       prefix=<filename>  prefix  for  the create files. The created files will have names ${prefix}_000000.bam,
       ${prefix}_000001.bam, etc.

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

       -1:    zlib/gzip default compression level

       0:     uncompressed

       1:     zlib/gzip level 1 (fast) compression

       9:     zlib/gzip level 9 (best) compression

       If libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-
       a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value
       is

       11:    igzip compression

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       bamsplit - split BAM files

       Report bugs to <germant@miltenyibiotec.de>

bamsplit [options]