Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR.

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 a

SUBMITTER: Beier S 

PROVIDER: S-EPMC9218589 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature