Man page - bamfilterflags(1)
Packages contains this manual
- bamadapterfind(1)
- bamchecksort(1)
- bamfilterflags(1)
- bamfixmateinformation(1)
- bammdnm(1)
- bamstreamingmarkduplicates(1)
- bamfillquery(1)
- bamseqchksum(1)
- bamtagconversion(1)
- bammerge(1)
- bamvalidate(1)
- bam12split(1)
- bammarkduplicates(1)
- bamalignfrac(1)
- bamsplit(1)
- bamfilterrg(1)
- bamdownsamplerandom(1)
- fastqtobam(1)
- bamzztoname(1)
- bamsormadup(1)
- bambisect(1)
- bamconsensus(1)
- bamrecalculatecigar(1)
- filtergtf(1)
- bammarkduplicates2(1)
- bamauxmerge2(1)
- normalisefasta(1)
- bamrecompress(1)
- bamcollate2(1)
- bamfilteraux(1)
- bamcat(1)
- bamsplitdiv(1)
- bam12strip(1)
- bammarkduplicatesopt(1)
- bamauxmerge(1)
- bam12auxmerge(1)
- bamrank(1)
- bamfiltermc(1)
- fastaexplod(1)
- bammaskflags(1)
- bamfeaturecount(1)
- bamclipreinsert(1)
- bamadapterclip(1)
- bamreset(1)
- bamintervalcomment(1)
- bamflagsplit(1)
- bamindex(1)
- bamfilterheader(1)
- bamranksort(1)
- bamtofastq(1)
- bamauxsort(1)
- bamfilterheader2(1)
- bamsort(1)
apt-get install biobambam2
Manual
BAMFILTERFLAGS
NAMESYNOPSIS
DESCRIPTION
AUTHOR
REPORTING BUGS
COPYRIGHT
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.