|FILTERGTF(1)||General Commands Manual||FILTERGTF(1)|
filtergtf - filter a gtf annotation file for use with bamfeaturecount
filtergtf < in.gtf > out.gtf [options]
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
Written by German Tischler-Höhle.
Report bugs to <email@example.com>
Copyright © 2009-2019 German Tischler-Höhle,
© 2011-2014 Genome Research Limited. License GPLv3+: GNU GPL version
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.