gtf

GTF stands for Gene Transfer Format, a widely used plain-text file format for describing gene annotations on a reference genome. It is a member of the General Feature Format (GFF) family and is most commonly encountered as a variant derived from GFF2. A GTF file describes features such as genes, transcripts, exons, and CDS regions, with coordinates tied to a specific assembly.

The file is tab-delimited and consists of nine fields per line: seqname (the reference sequence or chromosome), source (the annotation source), feature (such as gene, transcript, exon, CDS), start and end coordinates (1-based inclusive), score (a numeric value or .), strand (+ or −), frame (0, 1, 2 or . for no frame), and attributes (a semicolon-separated list of key-value pairs). The attributes commonly include gene_id, transcript_id, gene_name, and transcript_name, among others. The precise semantics depend on the feature type; for example, a gene feature marks the genomic span of a gene, while an exon feature denotes an exon of a transcript.

GTFs are central to genome annotation workflows and are widely used by genome browsers and annotation pipelines. They enable downstream analyses such as transcript assembly, expression quantification, and gene-model visualization. Although many projects now prefer the more flexible GFF3 format, GTF remains prevalent due to historical usage and compatibility with established tools. Converting between GTF and GFF3 and parsing GTF with various bioinformatics tools is common practice.