Analysis-ready VCF at Biobank scale using Zarr
Large row-encoded VCF files are a major bottleneck for current research, and storing and processing these files incurs a substantial cost. The VCF Zarr specification, building on widely used, open-source technologies, has the potential to greatly reduce these costs, and may enable a diverse ecosystem of next-generation tools for analysing genetic variation data directly from cloud-based object stores, while maintaining compatibility with existing file-oriented workflows.
Authors
- Jeff Hammerbacher (ORCID: https://orcid.org/0000-0001-6596-8563)
- Jerome Kelleher (ORCID: https://orcid.org/0000-0002-7894-5253)
- Tom White
- Jonny Hancox
- Per Unneberg (ORCID: https://orcid.org/0000-0001-5735-3315)
- Eric Czech (ORCID: https://orcid.org/0000-0002-4254-4255)
- Shadi Zabad (ORCID: https://orcid.org/0000-0002-8003-9284)
- Ben Jeffery (ORCID: https://orcid.org/0000-0002-1982-6801)
- Alistair Miles (ORCID: https://orcid.org/0000-0001-9018-4680)
- Benjamin Elsworth (ORCID: https://orcid.org/0000-0001-7328-4233)
- Timothy R. Millar (ORCID: https://orcid.org/0000-0002-5142-8811)
- Sam Tallman
- Rafal Wojdyla (ORCID: https://orcid.org/0009-0005-0735-7090)
- Konrad J. Karczewski (ORCID: https://orcid.org/0000-0003-2878-4671)
- Jérémy Guez (ORCID: https://orcid.org/0009-0007-6406-5187)
- Will Tyler
Institutions
- Broad Institute (US)
- Nvidia (United Kingdom) (GB)
- Plant & Food Research (NZ)
- Open Society Foundations (US)
- The George Institute for Global Health (GB)
- Science for Life Laboratory (SE)
- Ontario Genomics (CA)
- Wellcome Sanger Institute (GB)
- Morgan Stanley (United States) (US)
- University of Colorado Health (US)
- Massachusetts General Hospital (US)
- The White House (US)
- Genomics England (GB)
- McGill University (CA)
- University of Otago (NZ)
Publication Details
- Journal
- GigaScience
- Published
- 2025-01-01
- DOI
- https://doi.org/10.1093/gigascience/giaf049
- Citations
- 3
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 2.42
Funders
- Bill and Melinda Gates Foundation
- Knut och Alice Wallenbergs Stiftelse