{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T23:12:51Z","timestamp":1770419571688,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,10,28]],"date-time":"2021-10-28T00:00:00Z","timestamp":1635379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NSF Graduate Research Fellowship and the NIH","award":["R01 HG005855"],"award-info":[{"award-number":["R01 HG005855"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-2018-STG-804679"],"award-info":[{"award-number":["ERC-2018-STG-804679"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Inference of identity-by-descent (IBD) sharing along the genome between pairs of individuals has important uses. But all existing inference methods are based on genotypes, which is not ideal for low-depth Next Generation Sequencing (NGS) data from which genotypes can only be called with high uncertainty.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present a new probabilistic software tool, LocalNgsRelate, for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. Its inference is based on genotype likelihoods instead of genotypes, and thereby it takes the uncertainty of the genotype calling into account. Using real data from the 1000 Genomes project, we show that LocalNgsRelate provides more accurate IBD inference for low-depth NGS data than two state-of-the-art genotype-based methods, Albrechtsen et\u00a0al. (2009) and hap-IBD. We also show that the method works well for NGS data down to a depth of 2\u00d7.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>LocalNgsRelate is freely available at https:\/\/github.com\/idamoltke\/LocalNgsRelate.<\/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\/btab732","type":"journal-article","created":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T11:09:48Z","timestamp":1635160188000},"page":"1159-1161","source":"Crossref","is-referenced-by-count":9,"title":["LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9586-1027","authenticated-orcid":false,"given":"Alissa L","family":"Severson","sequence":"first","affiliation":[{"name":"Department of Genetics, Stanford University , Stanford, CA 94305-5020, USA"}]},{"given":"Thorfinn Sand","family":"Korneliussen","sequence":"additional","affiliation":[{"name":"GLOBE Institute, University of Copenhagen , 1350 Copenhagen K, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7052-8554","authenticated-orcid":false,"given":"Ida","family":"Moltke","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Copenhagen , 2200 Copenhagen N, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2021,10,28]]},"reference":[{"key":"2023020108514234900_btab732-B1","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/gepi.20378","article-title":"Relatedness mapping and tracts of relatedness for genome-wide data in the presence of LD","volume":"33","author":"Albrechtsen","year":"2009","journal-title":"Genet. Epidemiol"},{"key":"2023020108514234900_btab732-B2","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1534\/genetics.110.113977","article-title":"Natural selection and the distribution of identity-by-descent in the human genome","volume":"186","author":"Albrechtsen","year":"2010","journal-title":"Genetics"},{"key":"2023020108514234900_btab732-B3","doi-asserted-by":"crossref","first-page":"3855","DOI":"10.1093\/bioinformatics\/btz200","article-title":"ngsLD: evaluating linkage disequilibrium using genotype likelihoods","volume":"35","author":"Fox","year":"2019","journal-title":"Bioinformatics"},{"key":"2023020108514234900_btab732-B4","doi-asserted-by":"crossref","first-page":"4009","DOI":"10.1093\/bioinformatics\/btv509","article-title":"NgsRelate: a software tool for estimating pairwise relatedness from NGS data","volume":"31","author":"Korneliussen","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020108514234900_btab732-B5","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/s12859-014-0356-4","article-title":"ANGSD: analysis of Next Generation Sequencing Data","volume":"15","author":"Korneliussen","year":"2014","journal-title":"BMC Bioinform"},{"key":"2023020108514234900_btab732-B6","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.tig.2014.12.002","article-title":"Accounting for uncertainty in DNA sequencing data","volume":"31","author":"O\u2019Rawe","year":"2015","journal-title":"Trends Genet"},{"key":"2023020108514234900_btab732-B7","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1016\/j.ajhg.2020.02.010","article-title":"A fast and simple method for detecting identity by descent segments in large-scale data","volume":"106","author":"Zhou","year":"2020","journal-title":"Am. 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Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab732\/40978205\/btab732.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1159\/49008025\/btab732.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1159\/49008025\/btab732.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,11]],"date-time":"2023-11-11T18:01:35Z","timestamp":1699725695000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/4\/1159\/6413625"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,10,28]]},"references-count":7,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2022,1,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab732","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,15]]},"published":{"date-parts":[[2021,10,28]]}}}