ArticleBioinformatics (Oxford, England)2016
BGT: efficient and flexible genotype query across many samples.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review.PloS one · 2020Pooled it
- An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- Article
- DynamicbioRxiv : the preprint server for biology · 2025Article
- 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
- IGD: a simple, efficient genotype data format.Bioinformatics advances · 2025Article
- The scalable variant call representation: enabling genetic analysis beyond one million genomes.Bioinformatics (Oxford, England) · 2024Article
- GSC: efficient lossless compression of VCF files with fast query.GigaScience · 2024Article
- μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.Bioinformatics (Oxford, England) · 2023Article
- Data Structures for SMEM-Finding in the PBWT.International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium) · 2023Article
- GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species.Genome biology · 2023Article
- Exploiting parallelization in positional Burrows-Wheeler transform (PBWT) algorithms for efficient haplotype matching and compression.Bioinformatics advances · 2023Article
- A novel splice-affectingThe Lancet regional health. Europe · 2023Article
- XSI-a genotype compression tool for compressive genomics in large biobanks.Bioinformatics (Oxford, England) · 2022Article
- d-PBWT: dynamic positional Burrows-Wheeler transform.Bioinformatics (Oxford, England) · 2021Article
- VariantStore: an index for large-scale genomic variant search.Genome biology · 2021Article
- Sparse Project VCF: efficient encoding of population genotype matrices.Bioinformatics (Oxford, England) · 2021Article
- Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset.Bioinformatics (Oxford, England) · 2020Article
- Genotype imputation using the Positional Burrows Wheeler Transform.PLoS genetics · 2020Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
unlabelledBGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes the haplotypes of 32 488 samples across 39.2 million SNPs into a 7.4 GB database and decodes up to 420 million genotypes per CPU second. The high performance enables real-time responses to complex queries. AVAILABILITY AND IMPLEMENTATION: https://github.com/lh3/bgt.
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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.