GT-BED_TO_GFF3(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 GT-BED_TO_GFF3 💖

okay bestie, welcome to gt-bed_to_gff3 — it's a page in the GenomeTools Manual, and it's literally just here to help you turn your BED files into GFF3. glow-up for your data, fr fr. ✨

🌸 NAME 🌸

gt-bed_to_gff3 — parse a BED file and convert it to GFF3. that's it, that's the whole job, and she does it gorgeously. 💅

🦋 SYNOPSIS 🦋

gt bed_to_gff3 [BED_file]

so you run gt bed_to_gff3 and hand it a BED_file (that one's optional in the synopsis, iykyk, but that's how it's written so that's how we're keeping it). 🫶

✨ DESCRIPTION ✨

here's the thing, bestie — this command takes your BED file and gives you GFF3 back. and it has options. so many options. and we are NOT skipping a single one, because every flag is a main character here. 👑

  • -featuretype [string] — sets the type of your parsed BED features. the default is BED_feature. that's her name unless you rename her. 🎀
  • -thicktype [string] — sets the type of your parsed thick BED features (thicc features, we love them). default is BED_thick_feature. 💜
  • -blocktype [string] — sets the type of your parsed BED blocks. default is BED_block. blocks stay blocking. 🧱
  • -o [filename] — redirects output to the file you name. default is undefined, so if you don't say where, it's going where it goes. 🙈
  • -gzip [yes|no] — writes a gzip-compressed output file. default is no. say yes if you want your output zipped up cute. 🗜️
  • -bzip2 [yes|no] — writes a bzip2-compressed output file. default is no. a whole different compression vibe. 🌈
  • -force [yes|no] — forces writing to the output file. default is no. this one is for when the output file is being stubborn about existing. ⚠️
  • -help — displays help and exits. the classic. always there for you. 🫶
  • -version — displays version information and exits. hello, who are you, what version are you. 👋
not me reminding you that -force will make it write even when it normally wouldn't — that's the whole point of force, bestie. use it with intention. 💀

😭 REPORTING BUGS 😭

found a bug? do NOT suffer in silence, take it straight to https://github.com/genometools/genometools/issues and report it. the maintainers want to know. periodt. 🔥

so yeah — this whole page is from GenomeTools 1.6.6, dated 11/09/2025, and it lives in the GenomeTools Manual as page GT-BED_TO_GFF3(1). mwah, go convert something. 💋

📦 where this page comes from