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 <tischler@mpi-cbg.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.