bamsplit - split BAM files
bamsplit [options]
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
Written by German Tischler.
Report bugs to <
[email protected]>
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.