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.

BIOBAMBAM                                          August 2019                                      FILTERGTF(1)