gtf2json

A simple CLI utility to convert a GTF file to NDJSON for fast parsing

Summary

The GTF file format is fantastic when working with bedtools since it is essentially a modified version of the BED file format.

However, if you're interested in the annotations column, it can be a massive headache to parse - especially if you're operating on the full genome.

I wrote this tool to convert the GTF file format into streamable newline-delim JSON.

This makes it convenient to load with polars in python incredibly fast and skip all the annotation parsing.

Installation

You can install this with the rust package manager cargo:

cargo install gtf2json

Usage

# classic i/o
gtf2json -i <input.gtf> -o output.json

# write to stdout
gtf2json -i <input.gtf>