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BAMFLAGSPLIT(1) General Commands Manual BAMFLAGSPLIT(1)

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 end reads are placed in the single file
(partially) unmapped read pairs (pairs where at least one of the two mates is unmapped) are placed in the unmapped file
orphan reads (pairs where the other mate is missing in the file) are placed in the orphan file
supplementary mappings (mappings which have the supplementary flag set) are placed in the supplementary file
split pair reads (pairs such that the two ends map to different reference sequences/chromosomes) are placed in the split file
read pairs such that both ends map to the same strand are placed in the samestrand file
improperly mapped read pairs (read pairs where the mapped as a proper pair flag is not set) are place in the improper file
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 (see http://samtools.sourceforge.net/SAM1.pdf)
SAM (see http://samtools.sourceforge.net/SAM1.pdf)
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.

June 2014 BIOBAMBAM