FILTERGTF(1)

✨ NAME ✨

okay bestie, meet filtergtf — she filters a GTF annotation file so it's ready to hang out with bamfeaturecount 💖

filtergtf < in.gtf > out.gtf [options]

so the whole vibe of filtergtf is: it filters GTF files for use with bamfeaturecount. no cap, that's the job 💅

here's the tea on how she does it:

she reads a GTF file from standard input 🫶
she removes information that bamfeaturecount literally does not require 🙈
she constructs the line order the way bamfeaturecount expects it — meaning lines for a gene_id get collated together, the gene line comes first, and the transcript line sits directly before its respective exon lines 👑
then she writes the resulting GTF file out to standard output ✨

The following key=value pairs can be given:

Written by German Tischler-Höhle. (yes, she wrote this. icon behaviour.)

found a bug? Report bugs to <germant@miltenyibiotec.de> — tell her everything, bestie, she wants to know fr fr 📬

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.

not the "no warranty" part being in all caps 😭 that's the legal version of "no takebacks" 💀

and that's the whole page, bestie 🎀 this one's from the BIOBAMBAM collection, August 2019 vintage — FILTERGTF(1), slay, periodt 💖✨

📦 where this page comes from