{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:37Z","timestamp":1753875877573,"version":"3.41.2"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T00:00:00Z","timestamp":1699920000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universidad de la Rep\u00fablica; Ramon y Cajal","award":["RYC2019-028578-I"],"award-info":[{"award-number":["RYC2019-028578-I"]}]},{"name":"Gipuzkoa Fellows","award":["2022-FELL-000003\u201301","PID2021-126718OA-I00","PID2019-104958RB-C41"],"award-info":[{"award-number":["2022-FELL-000003\u201301","PID2021-126718OA-I00","PID2019-104958RB-C41"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Single-nucleotide variants (SNVs) are the most common type of genetic variation in the human genome. Accurate and efficient detection of SNVs from next-generation sequencing (NGS) data is essential for various applications in genomics and personalized medicine. However, SNV calling methods usually suffer from high computational complexity and limited accuracy. In this context, there is a need for new methods that overcome these limitations and provide fast reliable results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present EMVC-2, a novel method for SNV calling from NGS data. EMVC-2 uses a multi-class ensemble classification approach based on the expectation\u2013maximization algorithm that infers at each locus the most likely genotype from multiple labels provided by different learners. The inferred variants are then validated by a decision tree that filters out unlikely ones. We evaluate EMVC-2 on several publicly available real human NGS data for which the set of SNVs is available, and demonstrate that it outperforms state-of-the-art variant callers in terms of accuracy and speed, on average.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>EMVC-2 is coded in C and Python, and is freely available for download at: https:\/\/github.com\/guilledufort\/EMVC-2. EMVC-2 is also available in Bioconda.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad681","type":"journal-article","created":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T18:44:54Z","timestamp":1699987494000},"source":"Crossref","is-referenced-by-count":0,"title":["EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6125-5603","authenticated-orcid":false,"given":"Guillermo","family":"Dufort y \u00c1lvarez","sequence":"first","affiliation":[{"name":"INCO, Facultad de Ingenier\u00eda, Universidad de la Rep\u00fablica , Montevideo 11300, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mart\u00ed","family":"Xargay-Ferrer","sequence":"additional","affiliation":[{"name":"SPCOM Group, Universitat Polit\u00e8cnica de Catalunya \u2013 BarcelonaTech (UPC) , 08034 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alba","family":"Pag\u00e8s-Zamora","sequence":"additional","affiliation":[{"name":"SPCOM Group, Universitat Polit\u00e8cnica de Catalunya \u2013 BarcelonaTech (UPC) , 08034 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Idoia","family":"Ochoa","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, Tecnun, University of Navarra , 20018 Donostia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,11,14]]},"reference":[{"key":"2024030721360667600_btad681-B1","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1038\/s41587-021-00861-3","article-title":"A unified haplotype-based method for accurate and comprehensive variant calling","volume":"39","author":"Cooke","year":"2021","journal-title":"Nat 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