nonVCF

NonVCF is a term used in genomics to describe data representations that do not conform to the Variant Call Format (VCF). VCF is a widely adopted, text-based standard for describing small-scale genetic variants, but many data types and complex variants are not easily captured by VCF alone. NonVCF encompasses alternative formats and models used when VCF’s allele-centric encoding proves limiting or insufficient for the research question.

Examples of nonVCF data include raw alignment and read-level evidence (BAM/CRAM), assembly- or graph-based representations, and richer descriptions of variation such as structural variants, copy number changes, and haplotype structure. Formats frequently cited in discussions of nonVCF include Genome Variation Format (GVF), BED and BEDPE for genomic intervals and breakpoints, GFF/GTF for gene models and features, and graph-based formats like Graph Alignment/Graphical Fragment Assembly (GFA). In some workflows, nonVCF data is stored and exchanged using JSON-based representations or specialized databases that preserve contextual metadata not easily encoded in VCF.

Use cases for nonVCF approaches include complex structural variation, multi-allelic loci, pan-genome analyses, and graph-based references where variation is represented as paths or graphs rather than a single reference allele. Advantages include richer metadata and more flexible representations; drawbacks include reduced interoperability, tool support, and potential information loss in conversions to VCF.

Overall, nonVCF describes a family of data formats and models that complement VCF by addressing limitations in representing genomic variation, especially for complex, non-allelic, or graph-based scenarios.