Provided by: biobambam2_2.0.183+ds-1_amd64 
NAME
bamflagsplit - sort BAM files by coordinate or query name
SYNOPSIS
bamflagsplit [options]
DESCRIPTION
bamflagsplit reads a name collated BAM, SAM or CRAM file and distributes the contained reads into a set
of BAM files. The reads are distributed as follows:
single single end reads are placed in the single file
unmapped
(partially) unmapped read pairs (pairs where at least one of the two mates is unmapped) are placed
in the unmapped file
orphan orphan reads (pairs where the other mate is missing in the file) are placed in the orphan file
supplementary
supplementary mappings (mappings which have the supplementary flag set) are placed in the
supplementary file
split split pair reads (pairs such that the two ends map to different reference sequences/chromosomes)
are placed in the split file
samestrand
read pairs such that both ends map to the same strand are placed in the samestrand file
improper
improperly mapped read pairs (read pairs where the mapped as a proper pair flag is not set) are
place in the improper file
proper properly mapped pairs are placed in the proper file
The following key=value pairs can be given:
I=<[stdin]>: input filename, standard input if unset.
level=<-1|0|1|9|11>: set compression level of the output BAM files. 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
disablevalidation=<0|1>: sets whether input validation is performed. Valid values are
0: validation is enabled (default)
1: validation is disabled
single=<filename>: file name for the single file
singlemd5=<0|1>: md5 checksum creation for single output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given
file. If splitmd5filename, then no checksum will be computed.
unmapped=<filename>: file name for the unmapped file
unmappedmd5=<0|1>: md5 checksum creation for unmapped output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given
file. If splitmd5filename, then no checksum will be computed.
orphan=<filename>: file name for the orphan file
orphanmd5=<0|1>: md5 checksum creation for orphan output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given
file. If splitmd5filename, then no checksum will be computed.
supplementary=<filename>: file name for the supplementary file
supplementarymd5=<0|1>: md5 checksum creation for supplementary output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given
file. If splitmd5filename, then no checksum will be computed.
split=<filename>: file name for the split file
splitmd5=<0|1>: md5 checksum creation for split output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the splitmd5filename key is set, then the checksum is written to the given
file. If splitmd5filename, then no checksum will be computed.
samestrand=<filename>: file name for the samestrand file
samestrandmd5=<0|1>: md5 checksum creation for samestrand output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the samestrandmd5filename key is set, then the checksum is written to the
given file. If samestrandmd5filename, then no checksum will be computed.
improper=<filename>: file name for the improper file
impropermd5=<0|1>: md5 checksum creation for improper output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the impropermd5filename key is set, then the checksum is written to the given
file. If impropermd5filename, then no checksum will be computed.
proper=<filename>: file name for the proper file
propermd5=<0|1>: md5 checksum creation for proper output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the propermd5filename key is set, then the checksum is written to the given
file. If propermd5filename, then no checksum will be computed.
inputformat=<bam>: input file format. All versions of bamflagsplit come with support for the BAM input
format. If the program in addition is linked to the io_lib package, then the following options are valid:
bam: BAM (see http://samtools.sourceforge.net/SAM1.pdf)
sam: SAM (see http://samtools.sourceforge.net/SAM1.pdf)
cram: CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)
AUTHOR
Written by German Tischler.
REPORTING BUGS
Report bugs to <germant@miltenyibiotec.de>
COPYRIGHT
Copyright © 2009-2014 German Tischler, © 2011-2014 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 June 2014 BAMFLAGSPLIT(1)