ArticleBioinformatics (Oxford, England)2024
The scalable variant call representation: enabling genetic analysis beyond one million genomes.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- AlphaGenome Atlas:medRxiv : the preprint server for health sciences · 2026Article
- Article
- WxS-QC-a quality control pipeline for human germline short-variant Whole-Genome and Whole-Exome cohorts for population-scale analyses.Bioinformatics (Oxford, England) · 2026Article
- Genetic Determinants of Severe Hypertriglyceridemia: Rare Variants inInternational journal of molecular sciences · 2026Article
- Integrating 730,947 exome sequences with clinical literature improves gene discovery.medRxiv : the preprint server for health sciences · 2026Article
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- Diagnosing missed cases of spinal muscular atrophy in genome, exome, and panel sequencing data sets.Genetics in medicine : official journal of the American College of Medical Genetics · 2025Article
- 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
- One score to rule them all: regularized ensemble polygenic risk prediction with GWAS summary statistics.bioRxiv : the preprint server for biology · 2024Article
- Diagnosing missed cases of spinal muscular atrophy in genome, exome, and panel sequencing datasets.medRxiv : the preprint server for health sciences · 2024Article
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Abstract
motivationThe Variant Call Format (VCF) is widely used in genome sequencing but scales poorly. For instance, we estimate a 150 000 genome VCF would occupy 900 TiB, making it costly and complicated to produce, analyze, and store. The issue stems from VCF's requirement to densely represent both reference-genotypes and allele-indexed arrays. These requirements lead to unnecessary data duplication and, ultimately, very large files.
resultsTo address these challenges, we introduce the Scalable Variant Call Representation (SVCR). This representation reduces file sizes by ensuring they scale linearly with samples. SVCR's linear scaling relies on two techniques, both necessary for linearity: local allele indices and reference blocks, which were first introduced by the Genomic Variant Call Format. SVCR is also lossless and mergeable, allowing for N + 1 and N + K incremental joint-calling. We present two implementations of SVCR: SVCR-VCF, which encodes SVCR in VCF format, and VDS, which uses Hail's native format. Our experiments confirm the linear scalability of SVCR-VCF and VDS, in contrast to the super-linear growth seen with standard VCF files. We also discuss the VDS Combiner, a scalable, open-source tool for producing a VDS from GVCFs and unique features of VDS which enable rapid data analysis. SVCR, and VDS in particular, ensure the scientific community can generate, analyze, and disseminate genetics datasets with millions of samples. AVAILABILITY AND IMPLEMENTATION: https://github.com/hail-is/hail/.
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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.