Converting different annotation file formats (GTF/GFF/BED) to each other

Question

[Javad]

Hello everybody,

What is the most efficient way to convert different annotation file formats to each other.

GFF --> GTF

GTF --> BED

Thanks in advance.

[Pierre Lindenbaum]

• Convertion Of Gff3 To Gtf
• How To Convert Gencode Gtf Into Bed Format ?

[Javad]

Thanks It was very helpful.

[alejandrogzi]

If you need to reverse the conversion (e.g. BED -> GTF), here is recently developed tool written in rust bed2gtf

[alejandrogzi]

now there is also bed2gff if you want to convert .bed files to .gff3 files!