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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.


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Copyright © 2009-2019 German Tischler-Höhle, © 2011-2014 Genome Research Limited. License GPLv3+: GNU GPL version 3 <>
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