ArticleNature genetics2017
Graphtyper enables population-scale genotyping using pangenome graphs.
Article in Nature genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 177 papers, 10 of them syntheses that pooled it.
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Who cites it
177 citing papers in PubMed, 10 syntheses or guidelines pooled it.
- Multi-ancestry whole genome sequencing analysis of lean body mass.Genome biology · 2025Pooled it
- Multi-ancestry sequencing-based genome-wide association study of C-reactive protein in 513,273 genomes.Nature communications · 2025Pooled it
- Missense variants in FRS3 affect body mass index in populations of diverse ancestries.Nature communications · 2025Pooled it
- GWAS meta-analysis reveals key risk loci in essential tremor pathogenesis.Communications biology · 2024Pooled it
- Sequence variant affects GCSAML splicing, mast cell specific proteins, and risk of urticaria.Communications biology · 2023Pooled it
- A genome-wide meta-analysis identifies 50 genetic loci associated with carpal tunnel syndrome.Nature communications · 2022Pooled it
- A genome-wide meta-analysis uncovers six sequence variants conferring risk of vertigo.Communications biology · 2021Pooled it
- Eleven genomic loci affect plasma levels of chronic inflammation marker soluble urokinase-type plasminogen activator receptor.Communications biology · 2021Pooled it
- A meta-analysis uncovers the first sequence variant conferring risk of Bell's palsy.Scientific reports · 2021Pooled it
- A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis.Communications biology · 2021Pooled it
- Association mapping and genome prediction reveal a complex genetic architecture for resistance to black and frosty pod rot in cacao (Theobroma cacao L.) populations.The plant genome · 2026Article
- An Icelandic pangenome reference.Nature · 2026Article
- Genome-wide mapping of common and rare variant effects on adiposity across childhood.Nature genetics · 2026Article
- Whole genome sequencing of 1427 Mexican individuals from the oriGen cohort.Nature communications · 2026Article
- Genetic architecture of cytokine autoantibodies and associated risk of common diseases.Nature communications · 2026Article
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- Conditionally Significant eQTL and TWAS Analyses Identify MsRD26 as a Major Candidate Positive Regulator of Salt Tolerance in Medicago sativa L.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Sex-Specific Landscapes of Crossover and Noncrossover Recombination in Coppery Titi Monkeys (Plecturocebus cupreus).Genome biology and evolution · 2026Article
- The genetic architecture of fibromyalgia across 2.5 million individuals.Nature medicine · 2026Article
- Nanopore sequencing identifies parent-of-origin specific age-associated methylation changes at imprinted loci in the human genome.Nature communications · 2026Article
117 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A fundamental requirement for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to use this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in the whole genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in both small and population-scale sequencing studies.
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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.