Man page - bamsplitdiv(1)
Packages contas this manual
- bammarkduplicates2(1)
- bam12strip(1)
- filtergtf(1)
- bamrecalculatecigar(1)
- bamadapterclip(1)
- bamfilterheader(1)
- bamintervalcomment(1)
- normalisefasta(1)
- bamtagconversion(1)
- bamchecksort(1)
- bammaskflags(1)
- bam12split(1)
- bamauxmerge(1)
- bamfixmateinformation(1)
- bammarkduplicatesopt(1)
- bamdownsamplerandom(1)
- bamflagsplit(1)
- bamsplit(1)
- bamreset(1)
- bamzztoname(1)
- bamvalidate(1)
- bamindex(1)
- bamrank(1)
- bamadapterfind(1)
- bamseqchksum(1)
- bamalignfrac(1)
- bamstreamingmarkduplicates(1)
- bam12auxmerge(1)
- bamranksort(1)
- bammerge(1)
- bamconsensus(1)
- bamsort(1)
- bamauxsort(1)
- bammarkduplicates(1)
- bamsplitdiv(1)
- bamsormadup(1)
- bamcollate2(1)
- bamauxmerge2(1)
- bamfiltermc(1)
- bamclipreinsert(1)
- fastqtobam(1)
- bamrecompress(1)
- bamfilterheader2(1)
- bamfeaturecount(1)
- bamfillquery(1)
- bamfilteraux(1)
- bamfilterrg(1)
- bamfilterflags(1)
- fastaexplod(1)
- bambisect(1)
- bamtofastq(1)
- bamcat(1)
- bammdnm(1)
apt-get install biobambam2
Manual
| BAMSPLITDIV(1) | General Commands Manual | BAMSPLITDIV(1) |
NAME
bamsplitdiv - split BAM file into a set of BAM files
SYNOPSIS
bamsplitdiv [options]
DESCRIPTION
bamsplitdiv reads a BAM file via standard input and creates a set of output BAM files containing the alignments in the input. Given a positive natural number div bamsplitdiv will create div files. The alignments in the input file will be distributed to the output files in a round robin type scheme, i.e. entries 0, div, 2div, 3div, etc. will be written to the first output file, 1,div+1,2div+1, 3div+1, etc. to the second etc.
The following key=value pairs can be given:
div=<1>: number of output files
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
AUTHOR
Written by German Tischler.
REPORTING BUGS
Report bugs to <germant@miltenyibiotec.de>
COPYRIGHT
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.
| October 2013 | BIOBAMBAM |