Man page - filtergtf(1)
Packages contas this manual
- bammarkduplicates2(1)
- bam12strip(1)
- filtergtf(1)
- bamrecalculatecigar(1)
- bamadapterclip(1)
- bamfilterheader(1)
- bamintervalcomment(1)
- normalisefasta(1)
- bamtagconversion(1)
- bamchecksort(1)
- bammaskflags(1)
- bam12split(1)
- bamauxmerge(1)
- bamfixmateinformation(1)
- bammarkduplicatesopt(1)
- bamdownsamplerandom(1)
- bamflagsplit(1)
- bamsplit(1)
- bamreset(1)
- bamzztoname(1)
- bamvalidate(1)
- bamindex(1)
- bamrank(1)
- bamadapterfind(1)
- bamseqchksum(1)
- bamalignfrac(1)
- bamstreamingmarkduplicates(1)
- bam12auxmerge(1)
- bamranksort(1)
- bammerge(1)
- bamconsensus(1)
- bamsort(1)
- bamauxsort(1)
- bammarkduplicates(1)
- bamsplitdiv(1)
- bamsormadup(1)
- bamcollate2(1)
- bamauxmerge2(1)
- bamfiltermc(1)
- bamclipreinsert(1)
- fastqtobam(1)
- bamrecompress(1)
- bamfilterheader2(1)
- bamfeaturecount(1)
- bamfillquery(1)
- bamfilteraux(1)
- bamfilterrg(1)
- bamfilterflags(1)
- fastaexplod(1)
- bambisect(1)
- bamtofastq(1)
- bamcat(1)
- bammdnm(1)
apt-get install biobambam2
Manual
| FILTERGTF(1) | General Commands Manual | FILTERGTF(1) |
NAME
filtergtf - filter a gtf annotation file for use with bamfeaturecount
SYNOPSIS
filtergtf < in.gtf > out.gtf [options]
DESCRIPTION
filtergtf filters GTF files for use with bamfeaturecount. It reads a GTF file from standard input, removes information not required by bamfeaturecount, constructs the line order as expected by bamfeaturecount (lines for a gene_id collated, gene line first, transcript line directly before their respective exon lines) and writes the resulting GTF file to standard output.
The following key=value pairs can be given:
T=<filename>: set the prefix for temporary file names
AUTHOR
Written by German Tischler-Höhle.
REPORTING BUGS
Report bugs to <germant@miltenyibiotec.de>
COPYRIGHT
Copyright © 2009-2019 German Tischler-Höhle,
© 2011-2014 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.
| August 2019 | BIOBAMBAM |