{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,20]],"date-time":"2025-08-20T12:57:54Z","timestamp":1755694674009,"version":"3.37.3"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,4,21]],"date-time":"2020-04-21T00:00:00Z","timestamp":1587427200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Australian Postgraduate Award"},{"name":"National Health and Medical Research Council Career Development Fellowship","award":["1105271"],"award-info":[{"award-number":["1105271"]}]},{"name":"National Heart Foundation of Australia Future Leader Fellowships","award":["101204","100848"],"award-info":[{"award-number":["101204","100848"]}]},{"name":"NSW Health Early-Mid Career Fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In 2018, Google published an innovative variant caller, DeepVariant, which converts pileups of sequence reads into images and uses a deep neural network to identify single-nucleotide variants and small insertion\/deletions from next-generation sequencing data. This approach outperforms existing state-of-the-art tools. However, DeepVariant was designed to call variants within a single sample. In disease sequencing studies, the ability to examine a family trio (father-mother-affected child) provides greater power for disease mutation discovery.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To further improve DeepVariant\u2019s variant calling accuracy in family-based sequencing studies, we have developed a family-based variant calling pipeline, dv-trio, which incorporates the trio information from the Mendelian genetic model into variant calling based on DeepVariant.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>dv-trio is available via an open source BSD3 license at GitHub (https:\/\/github.com\/VCCRI\/dv-trio\/).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>e.giannoulatou@victorchang.edu.au<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa116","type":"journal-article","created":{"date-parts":[[2020,4,17]],"date-time":"2020-04-17T19:11:49Z","timestamp":1587150709000},"page":"3549-3551","source":"Crossref","is-referenced-by-count":12,"title":["dv-trio: a family-based variant calling pipeline using DeepVariant"],"prefix":"10.1093","volume":"36","author":[{"given":"Eddie K K","family":"Ip","sequence":"first","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"},{"name":"St. Vincent\u2019s Clinical School , UNSW Sydney, Sydney, Australia"}]},{"given":"Clinton","family":"Hadinata","sequence":"additional","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"}]},{"given":"Joshua W K","family":"Ho","sequence":"additional","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"},{"name":"St. Vincent\u2019s Clinical School , UNSW Sydney, Sydney, Australia"},{"name":"School of Biomedical Sciences , The University of Hong Kong, Hong Kong, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7084-6736","authenticated-orcid":false,"given":"Eleni","family":"Giannoulatou","sequence":"additional","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"},{"name":"St. Vincent\u2019s Clinical School , UNSW Sydney, Sydney, Australia"}]}],"member":"286","published-online":{"date-parts":[[2020,4,21]]},"reference":[{"key":"2023062300073957000_btaa116-B1","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1093\/bioinformatics\/btw576","article-title":"AKT: ancestry and kinship toolkit","volume":"33","author":"Arthur","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062300073957000_btaa116-B2","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat. 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