ArticleMolecular biology and evolution2021
Fast and Robust Identity-by-Descent Inference with the Templated Positional Burrows-Wheeler Transform.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Blocks of Identity by Descent Reveal the Dual Role Played by Reef Fish Larvae for Retention and Dispersal.Molecular ecology · 2026Article
- Recovering the precolonial population structure of Khoe-San descendant populations.Science advances · 2026Article
- Genetic dissection of grain yield and correlated proxy traits under suboptimal conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Updating the RZooRoH Package for the Analysis of Inbreeding, Identity-By-Descent and Relatedness From Genomic Data.Molecular ecology resources · 2026Article
- RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.Bioinformatics (Oxford, England) · 2026Article
- The genetic legacy of the 17th-century colonial capital of St. Mary's City.Current biology : CB · 2026Article
- HiFiMAP: High-resolution fast identity-by-descent mapping test.medRxiv : the preprint server for health sciences · 2026Article
- A novel method for across-chromosome phasing without relative data.Bioinformatics (Oxford, England) · 2026Article
- Linkage- and ROH-based genomic relationship matrices for IBD based management of genetic diversity.Genetics, selection, evolution : GSE · 2026Article
- Topological stratification of continuous genetic variation in large biobanks.PLoS genetics · 2026Article
- RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis.bioRxiv : the preprint server for biology · 2026Article
- Haplotype-based Parallel PBWT for Biobank Scale Data.IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences · 2026Article
- RaPID2: a parallel scalable framework for identity-by-descent segment detection via parallel PBWT.Bioinformatics advances · 2026Article
- 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
- No evidence for disassortative mating based on HLA in a small-scale, endogamous population.bioRxiv : the preprint server for biology · 2025Article
- Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses.HGG advances · 2025Article
- Recovering the pre-colonial population structure of Khoe-San descendant populations.bioRxiv : the preprint server for biology · 2025Article
- Identity-by-descent segments in large samples.Theoretical population biology · 2025Article
- SPC: a SPectral Component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis.medRxiv : the preprint server for health sciences · 2025Article
- Benchmarking and optimization of methods for the detection of identity-by-descent in high-recombiningeLife · 2025Article
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7 authors.
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Abstract
Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors, we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally, we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale data sets with millions of samples. Furthermore, we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis, exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for noncommercial use in the code repository (https://github.com/23andMe/phasedibd, last accessed January 11, 2021).
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