bamflagsplit1
Sort bam files by coordinate or query name
Usage
bamflagsplit [options]
Overview
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) |
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).