bammaskflags - remove flags from alignments
bammaskflags [options]
bammaskflags reads a BAM file from standard input, performs a bit wise and with
the flags field of each read/alignment and writes the resulting data to
standard output in BAM format.
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
Intel
article on igzip then an additional valid value is
- 11:
- igzip compression
maskneg=<0> mask of flags to be removed (a bit wise and is computed
between the bit complement of this number and the flag field of the
reads/alignments in the input BAM file). This value can be obtained by adding
up the following values of the flags:
- 1
- PAIRED (paired in sequencing)
- 2
- PROPER_PAIR (mapped as a proper pair)
- 4
- UNMAP (unmapped)
- 8
- MUNMAP (mate unmapped)
- 16
- REVERSE (mapped to the reverse strand)
- 32
- MREVERSE (mate mapped to the reverse strand)
- 64
- READ1 (first read of pair)
- 128
- READ2 (second read of pair)
- 256
- SECONDARY (secondary alignment)
- 512
- QCFAIL (failed quality control)
- 1024
- DUP (duplicate)
- 2048
- SUPPLEMENTARY (supplementary)
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.
auxexists=[taglist]: only mask records containing any of the given aux
field tags. taglist is a comma separated list of aux field names. Flag fields
of records are only filtered if the respective records contain any of the aux
fields mentioned in this list. By default all records are filtered. If e.g.
auxexists=AS is given, then only flag fields of records containing an AS aux
field are masked.
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.