{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:14Z","timestamp":1740185114505,"version":"3.37.3"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,2]],"date-time":"2021-12-02T00:00:00Z","timestamp":1638403200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1S10OD021644-01A1","5R01HG010757"],"award-info":[{"award-number":["1S10OD021644-01A1","5R01HG010757"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>We present trfermikit, a software tool designed to detect deletions larger than 50\u2009bp occurring in Variable Number Tandem Repeats using Illumina DNA sequencing reads. In such regions, it achieves a better tradeoff between sensitivity and false discovery than a state-of-the-art structural variation caller, Manta and complements it by recovering a significant number of deletions that Manta missed. trfermikit is based upon the fermikit pipeline, which performs read assembly, maps the assembly to the reference genome and calls variants from the alignment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/github.com\/petermchale\/trfermikit.<\/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\/btab805","type":"journal-article","created":{"date-parts":[[2021,11,27]],"date-time":"2021-11-27T20:09:21Z","timestamp":1638043761000},"page":"1231-1234","source":"Crossref","is-referenced-by-count":0,"title":["trfermikit: a tool to discover VNTR-associated deletions"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6452-1786","authenticated-orcid":false,"given":"Peter","family":"McHale","sequence":"first","affiliation":[{"name":"Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah , Salt Lake City, UT 84112, USA"}]},{"given":"Aaron R","family":"Quinlan","sequence":"additional","affiliation":[{"name":"Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah , Salt Lake City, UT 84112, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,12,2]]},"reference":[{"key":"2023020108544198900_btab805-B1"},{"key":"2023020108544198900_btab805-B2","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1038\/ng1197-350","article-title":"Insulin VNTR allele-specific effect in type 1 diabetes depends on identity of untransmitted paternal allele. 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