ArticleF1000Research2022
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR.
Article in F1000Research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them.Genome biology and evolution · 2026Article
- Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation.Bioinformatics (Oxford, England) · 2026Article
- Order from entropy: big data from FAIR data cohorts in the digital age of plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community.Database : the journal of biological databases and curation · 2025Article
- Article
- DivBrowse-interactive visualization and exploratory data analysis of variant call matrices.GigaScience · 2022Article
- On the way to plant data commons - a genotyping use case.Journal of integrative bioinformatics · 2022Article
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Authors and funding
15 authors.
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Abstract
In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. They form a basis for the proposed VCF extensions here. We have learned from the existing application of VCF that the definition of relevant metadata using controlled standards, vocabulary and the consistent use of cross-references via resolvable identifiers (machine-readable) are particularly necessary and propose their encoding. VCF is an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant data (for example, the HapMap and the gVCF formats), but none currently have the reach of VCF. For the sake of simplicity, we will only discuss VCF and our recommendations for its use, but these recommendations could also be applied to gVCF. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.
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