ArticleBioinformatics (Oxford, England)2021
Sparse Project VCF: efficient encoding of population genotype matrices.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Compressive pangenomics using mutation-annotated networks.Nature genetics · 2026Article
- Lessons from national biobank projects utilizing whole-genome sequencing for population-scale genomics.Genomics & informatics · 2025Review
- Analysis-ready VCF at Biobank scale using Zarr.bioRxiv : the preprint server for biology · 2025Article
- Analysis-ready VCF at Biobank scale using Zarr.GigaScience · 2025Article
- The scalable variant call representation: enabling genetic analysis beyond one million genomes.Bioinformatics (Oxford, England) · 2024Article
- The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes.bioRxiv : the preprint server for biology · 2024Article
- A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.PLoS computational biology · 2022Article
- Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes.Genetics · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
summaryVariant Call Format (VCF), the prevailing representation for germline genotypes in population sequencing, suffers rapid size growth as larger cohorts are sequenced and more rare variants are discovered. We present Sparse Project VCF (spVCF), an evolution of VCF with judicious entropy reduction and run-length encoding, delivering >10× size reduction for modern studies with practically minimal information loss. spVCF interoperates with VCF efficiently, including tabix-based random access. We demonstrate its effectiveness with the DiscovEHR and UK Biobank whole-exome sequencing cohorts. AVAILABILITY AND IMPLEMENTATION: Apache-licensed reference implementation: github.com/mlin/spVCF. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.