ArticleNature genetics2025
Locityper enables targeted genotyping of complex polymorphic genes.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- Article
- gaftools: a toolkit for analyzing and manipulating pangenome alignments.Bioinformatics (Oxford, England) · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Complex structural variation, phylogeny, and disease associations of the mucin pangenome.medRxiv : the preprint server for health sciences · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- Article
- Recent advances in understanding the spectrum of genetic determinants of lipoprotein(a) levels.Current opinion in lipidology · 2026Review
- Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.Genome biology and evolution · 2026Review
- Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.Nature genetics · 2025Article
- Population-scale Long-read Sequencing in themedRxiv : the preprint server for health sciences · 2025Article
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- Genotyping of selected germline adaptive immune system loci using short-read sequencing data.Genome research · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Complex genetic variation in nearly complete human genomes.bioRxiv : the preprint server for biology · 2024Article
- Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B.American journal of human genetics · 2024Article
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6 authors.
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Abstract
The human genome contains many structurally variable polymorphic loci, including several hundred disease-associated genes, almost inaccessible for accurate variant calling. Here we present Locityper, a tool capable of genotyping such challenging genes using short-read and long-read whole-genome sequencing. For each target, Locityper recruits and aligns reads to locus haplotypes, for instance, extracted from a pangenome, and finds the likeliest haplotype pair by optimizing read alignment, insert size and read depth profiles. Across 256 challenging medically relevant loci, Locityper achieves a median quality value (QV) above 35 from both long-read and short-read data, outperforming state-of-the-art Illumina and PacBio HiFi variant calling pipelines by 10.9 and 1.7 points, respectively. Furthermore, Locityper provides access to hyperpolymorphic HLA genes and other gene families, including KIR, MUC and FCGR. With its low running time of 1 h 35 m per sample at eight threads, Locityper is scalable to biobank-sized cohorts, enabling association studies for previously intractable disease-relevant genes.
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