Federated Genotype
Imputation Platform
African-led, African-hosted infrastructure for genotype imputation. Discover reference panels, access data, and run pipelines across federated nodes -- built on GA4GH and community standards.
How it works
Three GA4GH standard APIs, one seamless workflow
Discover
Data Connect
Query reference panels by build, population, and continent across federated nodes.
Access
DRS + Passport
Authenticate via SSO. Resolve DRS URIs for panels and input files with visa-based access control.
Compute
WES + RO-Crate
Submit imputation jobs to federated WES nodes. Track progress. Download results with full provenance.
Everything you need for genomic imputation
A federated platform connecting African compute infrastructure via GA4GH and community standards.
African-hosted, no cloud dependency
All infrastructure runs on ILIFU research cloud at the University of Cape Town. Data stays in South Africa under POPIA. Free for academic researchers.
Supported by NIH grant U24HG012750Provided to you by
Frequently asked questions
Who can use AfriGen-D FedImpute?+
Academic and non-profit researchers studying human genomics can register for free. Each controlled-access reference panel has its own Data Access Agreement (DAA) that must be accepted in-app before use.
Which reference panels are available?+
H3Africa v6 (full and African-only subsets) and H3Africa v7 for African-ancestry imputation. HapMap2 (CEU) is available for benchmarking. More panels are added as they are published by the H3Africa Consortium.
Where is my data stored?+
Uploaded VCFs, imputation results, and provenance records are stored on the ILIFU research cloud at the University of Cape Town, in compliance with POPIA and H3Africa governance. Reference panels never leave African infrastructure. You can download your own imputed results (encrypted with a one-time password) while they are available on the platform.
How long are my results kept?+
Input files are retained for 30 days after upload. Imputed results are retained for 7 days after completion. Results are encrypted with a one-time password delivered via email -- download them before expiry.
What file formats are supported?+
VCF or bgzipped VCF (.vcf.gz). Files must be sorted by chromosomal position, use a supported reference build (hg19 or hg38), and contain at least 20 samples.
Is there a cost?+
No. AfriGen-D FedImpute is free for academic researchers, supported by NIH grant U24HG012750.
How is this different from Michigan or TOPMed imputation servers?+
AfriGen-D is built on open GA4GH standards (DRS, WES, Passport, Data Connect) rather than a single-node REST API. This enables federation: the platform is designed so a single submission can run across multiple African nodes and panels. Reference panels are African-specific (H3Africa v6/v7) and data stays on African infrastructure.