BAMFIXMATEINFORMATION(1)

NAME
bamfixmateinformation - fix mate pair information in BAM files

SYNOPSIS

bamfixmateinformation [options]

DESCRIPTION
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.

AUTHOR
Written by German Tischler.

REPORTING BUGS
Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT
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.