NAME

       bamfilterrg - filter read groups from a BAM file

SYNOPSIS

       bamfilterrg [options]

DESCRIPTION

       bamfilterrg  reads  a  BAM  file from standard input, keeps the reads which belong to a given set of read
       groups and writes these reads to standard output in BAM format.

       The following key=value pairs can be given:

       readgroups=<[]>: list of read groups to be kept. Default is to keep all reads. Multiple read  groups  are
       separated by comma.

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       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

       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.

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.