GFFGTF

GFFGTF is a proposed unified genomic feature annotation data format intended to merge and extend the capabilities of the General Feature Format (GFF) and the Gene Transfer Format (GTF). It is designed to improve interoperability across genome annotation pipelines by providing a single representation that can accommodate both general feature annotations and transcript-centric records. The specification emphasizes backward compatibility through mapping rules from existing GFF3 and GTF data.

Format and syntax: GFFGTF retains a tab-delimited line structure with fields analogous to GFF and GTF: seqid, source, feature_type, start, end, score, strand, phase, and attributes. It extends the attributes field with mandatory feature_id, optional parent links, and dbxref cross-references, plus a version and assembly tag. The attributes are serialized as key=value pairs separated by semicolons. The format supports hierarchical relationships, explicit evidence metadata, and versioned annotations to aid reproducibility. Validation is intended to be enforced by a formal schema and accompanying validators.

Adoption and status: As of the latest community draft, GFFGTF has limited adoption and remains non-binding. Pilot projects have attempted conversions from legacy GFF3 and GTF files, and several tool developers have implemented provisional parsers and exporters. No universal standard has emerged, and some groups prefer existing formats due to ecosystem maturity.

Advantages and criticisms: Proponents cite unified semantics, easier cross-project comparisons, and streamlined validation workflows. Critics warn of added complexity, migration costs, and potential fragmentation if divergent variants appear.

See also: General Feature Format (GFF), Gene Transfer Format (GTF), GFF3, BED, Genomic annotation formats.