Provided by: biobambam2_2.0.185+ds-1_amd64 bug

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.