bamfilterflags - remove entries from BAM files matching a given set of flags
bamfilterflags [options]
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.
Written by German Tischler.
Report bugs to <
[email protected]>
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.