bamflagsplit - sort BAM files by coordinate or query name
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)
Written by German Tischler.
Report bugs to <germant@miltenyibiotec.de>
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.