bamfixmateinformation - fix mate pair information in BAM files
bamfixmateinformation [options]
bamfixmateinformation reads a BAM, SAM or CRAM file, fixes the mate pair
information of paired alignments and writes the resulting file as BAM, SAM or
CRAM. The input file must be sorted by query name (see bamsort).
bamfixmateinformation modifies the following fields for paired reads with
aligned mates:
- -
- mate alignment reference sequence id
- -
- mate alignment position on reference sequence
- -
- mate unmapped/mate mapped to reverse strand flags
- -
- MQ auxiliary tag denoting the mapping quality of the mapped
mate
- -
- inferred template length
The following key=value pairs can be given:
level=<-1|0|1|9|11>: set compression level of the output BAM file.
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
md5=<0|1>: md5 checksum creation for output file. This option can
only be given if outputformat=bam. Then valid values are
- 0:
- do not compute checksum. This is the default.
- 1:
- compute checksum. If the md5filename key is set, then the
checksum is written to the given file. If md5filename is unset, then no
checksum will be computed.
md5filename file name for md5 checksum if md5=1.
inputformat=<bam>: input file format. All versions of bamsort 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)
outputformat=<bam>: output file format. All versions of bamsort
come with support for the BAM output 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).
This format is not advisable for data sorted by query name.
I=<[stdin]>: input filename, standard input if unset.
O=<[stdout]>: output filename, standard output if unset.
inputthreads=<[1]>: input helper threads, only valid for
inputformat=bam.
outputthreads=<[1]>: output helper threads, only valid for
outputformat=bam.
reference=<[]>: reference FastA file for inputformat=cram and
outputformat=cram. An index file (.fai) is required.
Written by German Tischler.
Report bugs to <
[email protected]>
Copyright © 2009-2013 German Tischler, © 2011-2013 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.