BAMFILTERFLAGS

NAME

bamfilterflags - remove entries from BAM files matching a given set of flags

SYNOPSIS

bamfilterflags [options]

DESCRIPTION

bamfilterflags reads a BAM file from standard input, discards alignments matching a given set of flags and writes the remaining set of alignments to a BAM 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 additional threads used for rewriting if markthreads > 1, otherwise no parallelism will be employed.

exclude=<>: Do not include reads in the output that have any of the given flags set. The flags are given separated by commas. Valid flags are:

PAIRED:

read was paired in sequencing

PROPER_PAIR:

read has been mapped as part of a proper pair

	UNMAP:	read was not mapped
	MUNMAP:	mate of read was not mapped

REVERSE:

read was mapped to the reverse strand

MREVERSE:

mate of read was mapped to the reverse strand

	READ1:		read was first read of a pair during sequencing
	READ2:		read was second read of a pair during sequencing

SECONDARY:

alignment is secondary, i.e. an alternative mapping to the primary alignment in the same file

	QCFAIL:	read as marked as having failed quality control
	DUP:	read is marked as a duplicate of another read in the same file (see bammarkduplicates)

SUPPLEMENTARY:

read is marked as supplementary alignment

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.