BAMFILTERMC(1) | General Commands Manual | BAMFILTERMC(1) |
bamfiltermc - remove MC aux fields for reads with unmapped mates
bamfilterflags [options]
bamfiltermc reads a SAM/BAM/CRAM file from standard input, removes MC aux fields for reads with unmapped mates (which were erroneously inserted by earlier versions of biobambam2) and writes the resulting alignments to a SAM/BAM/CRAM file on the standard output stream.
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
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
numthreads=<1>: number of worker threads.
inputthreads=<1>: number of input threads.
outputthreads=<1>: number of output threads.
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.
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:
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:
Written by German Tischler.
Report bugs to <germant@miltenyibiotec.de>
Copyright © 2009-2016 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 2016 | BIOBAMBAM2 |