{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T22:52:03Z","timestamp":1773787923198,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T00:00:00Z","timestamp":1677456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM133805"],"award-info":[{"award-number":["R35GM133805"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, visualization and variant analysis frameworks are based on variant-level analysis and do not automatically handle these features. We present haptools, an open-source toolkit for performing local ancestry aware and haplotype-based analysis of complex traits. Haptools supports fast simulation of admixed genomes, visualization of admixture tracks, simulation of haplotype- and local ancestry-specific phenotype effects and a variety of file operations and statistics computed in a haplotype-aware manner.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Haptools is freely available at https:\/\/github.com\/cast-genomics\/haptools.<\/jats:p><\/jats:sec><jats:sec><jats:title>Documentation<\/jats:title><jats:p>Detailed documentation is available at https:\/\/haptools.readthedocs.io.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad104","type":"journal-article","created":{"date-parts":[[2023,2,25]],"date-time":"2023-02-25T05:47:44Z","timestamp":1677304064000},"source":"Crossref","is-referenced-by-count":15,"title":["Haptools: a toolkit for admixture and haplotype analysis"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3679-0345","authenticated-orcid":false,"given":"Arya R","family":"Massarat","sequence":"first","affiliation":[{"name":"Bioinformatics and Systems Biology Graduate Program, Department of Bioengineering, University of California San Diego , La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Lamkin","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of California San Diego , La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ciara","family":"Reeve","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California San Diego , La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0737-0533","authenticated-orcid":false,"given":"Amy L","family":"Williams","sequence":"additional","affiliation":[{"name":"23andMe, Inc. , Sunnyvale, CA 94086, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matteo","family":"D\u2019Antonio","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Department of Medicine, University of California San Diego , La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6086-3903","authenticated-orcid":false,"given":"Melissa","family":"Gymrek","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of California San Diego , La Jolla, CA 92093, USA"},{"name":"Department of Biomedical Informatics, Department of Medicine, University of California San Diego , La Jolla, CA 92093, USA"},{"name":"Department of Medicine, University of California San Diego , La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,2,27]]},"reference":[{"key":"2023030800003243700_","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/s41588-020-00766-y","article-title":"Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power","volume":"53","author":"Atkinson","year":"2021","journal-title":"Nat. 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