ArticleMolecular biology and evolution2023
HaploBlocks: Efficient Detection of Positive Selection in Large Population Genomic Datasets.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores.bioRxiv : the preprint server for biology · 2026Article
- Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution.Molecular biology and evolution · 2024Article
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10 authors.
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Abstract
Genomic regions under positive selection harbor variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets with hundreds of thousands of individuals or more. We have developed and implemented an efficient haplotype-based approach able to scan large datasets and accurately detect positive selection. We achieve this by combining a pattern matching approach based on the positional Burrows-Wheeler transform with model-based inference which only requires the evaluation of closed-form expressions. We evaluate our approach with simulations, and find it to be both sensitive and specific. The computational resource requirements quantified using UK Biobank data indicate that our implementation is scalable to population genomic datasets with millions of individuals. Our approach may serve as an algorithmic blueprint for the era of "big data" genomics: a combinatorial core coupled with statistical inference in closed form.
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