varmatapi

Varmatapi is a term used to describe a proposed open standard API and accompanying software ecosystem designed to provide uniform access to variant matrices in genomics. The goal is to standardize how genotype data, allele frequencies, variant annotations, and sample metadata are retrieved and manipulated across diverse data stores.

Core concepts define a data model that includes entities such as Variant, Genotype, Sample, and Matrix. API endpoints or queryable interfaces typically cover variants, samples, and matrix slices, with support for filtering, pagination, and streaming for large datasets. Data sources can include VCF/BCF files, HDF5-based matrices, or database-backed stores, with adapters that translate between stored formats and the common API model.

Architecturally, varmatapi envisions client libraries in multiple languages and server components that implement the interface, possibly exposing RESTful or GraphQL endpoints. Privacy and access control are considered, enabling tiered data sharing and fine-grained permissions. Interoperability with existing standards—such as GA4GH genomics APIs, VRS representations, and VCF conventions—is encouraged to promote compatibility with established tooling and pipelines.

Applications and impact include enabling more scalable GWAS workflows, seamless data integration across studies, and streamlined visualization and imputation pipelines. By providing a shared interface to variant matrices, varmatapi aims to reduce data wrangling and promote reusability of analysis components.

See also: Variant Call Format, GA4GH genomics APIs, Variant Matrix, Genomics Data Standards.