BAMFILTERMC(1)

NAME
bamfiltermc - remove MC aux fields for reads with unmapped mates

SYNOPSIS

bamfilterflags [options]

DESCRIPTION
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

-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

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

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.

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:

bam:
    BAM (see http://samtools.sourceforge.net/SAM1.pdf)

sam:
    SAM (see http://samtools.sourceforge.net/SAM1.pdf)

cram:
    CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit). This format is not advisable for data sorted by query name.

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:

bam:
    BAM (see http://samtools.sourceforge.net/SAM1.pdf)

sam:
    SAM (see http://samtools.sourceforge.net/SAM1.pdf)

cram:
    CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)

AUTHOR
Written by German Tischler.

REPORTING BUGS
Report bugs to <tischler@mpi-cbg.de>

COPYRIGHT
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.