BAMFILTERRG(1) | General Commands Manual | BAMFILTERRG(1) |
bamfilterrg - filter read groups from a BAM file
bamfilterrg [options]
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
level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are
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
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
md5filename file name for md5 checksum if md5=1.
index=<0|1>: compute BAM index for output file. Valid values are
indexfilename file name for BAM index if index=1.
Written by German Tischler.
Report bugs to <germant@miltenyibiotec.de>
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.
July 2013 | BIOBAMBAM |