NAME

       bammerge - merge BAM files

SYNOPSIS

       bammerge [options]

DESCRIPTION

       bammerge  reads  a set of input BAM files, merges the contained headers and alignment data
       and writes the output on standard output in BAM format. The input files can  be  specified
       via  the  I key. Any none key=value arguments given after the key=value pairs will also be
       considered as input files. The input files need to be sorted by coordinate or query  name.
       The  set  of  reference  sequences in the files does not need to be identical. For merging
       coordinate sorted files however the order of the reference sequences in the headers  needs
       to  be  consistent  among the files, i.e. if reference sequence A appears before reference
       sequence B in any input file, then this needs to hold for all other files as well. If  the
       order is not consistent then bammerge cannot be used for merging. In this case the merging
       can be done by concatenating the files using bamcat and running bamsort afterwards.

       The following key=value pairs can be given:

       I=<stdin>: name of the input file. This key can be used multiple times

       SO=<coordinate>: Sort order. By default the sort order is coordinate.

       coordinate:
              input files are sorted by coordinate. The created output file  will  be  sorted  by
              coordinate as well.

       queryname:
              input  files  are  sorted  by query name. The created output file will be sorted by
              query name as well.

       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

       tmpfile=<filename>: prefix for temporary files. By default the temporary files are created
       in the current directory

       md5=<0|1>: md5 checksum creation for output file. 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.

       index=<0|1>: compute BAM index for output file. Valid values are

       0:     do not compute BAM index. This is the default.

       1:     compute BAM index. If the indexfilename key is set, then the BAM index  is  written
              to the given file. If indexfilename is unset, then no BAM index will be computed.

       indexfilename file name for BAM index if index=1.

       IL  name of file containing input file names. The given text file contains a list of input
       file names, one file per line.

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.