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.