{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T23:08:19Z","timestamp":1775603299838,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T00:00:00Z","timestamp":1643932800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Senior Research Fellowship","award":["1116955"],"award-info":[{"award-number":["1116955"]}]},{"DOI":"10.13039\/501100023250","name":"Lorenzo and Pamela Galli Charitable Trust","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100023250","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1188098"],"award-info":[{"award-number":["1188098"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Victorian State Government Operational Infrastructure Support"},{"name":"Australian Government NHMRC Independent Research Institute Infrastructure Support"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>StructuralVariantAnnotation is an R\/Bioconductor package that provides a framework for decoupling downstream analysis of structural variant breakpoints from upstream variant calling methods. It standardizes the representational format from BEDPE, or any of the three different notations supported by VCF into a breakpoint GRanges data structure suitable for use by the wider Bioconductor ecosystem. It handles both transitive breakpoints and duplication\/insertion notational differences of identical variants\u2014both common scenarios when comparing short\/long read-based call sets that confound downstream analysis. StructuralVariantAnnotation provides the caller-agnostic foundation needed for a R\/Bioconductor ecosystem of structural variant annotation, classification and interpretation tools able to handle both simple and complex genomic rearrangements.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>StructuralVariantAnnotation is implemented in R and available for download as the Bioconductor StructuralVariantAnnotation package. Details can be found at https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/StructuralVariantAnnotation.html. It has been released under a GPL license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac042","type":"journal-article","created":{"date-parts":[[2022,1,28]],"date-time":"2022-01-28T12:13:07Z","timestamp":1643371987000},"page":"2046-2048","source":"Crossref","is-referenced-by-count":9,"title":["StructuralVariantAnnotation: a R\/Bioconductor foundation for a caller-agnostic structural variant software ecosystem"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0951-7116","authenticated-orcid":false,"given":"Daniel L","family":"Cameron","sequence":"first","affiliation":[{"name":"The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"},{"name":"Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1433-0484","authenticated-orcid":false,"given":"Ruining","family":"Dong","sequence":"additional","affiliation":[{"name":"The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"},{"name":"Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1102-8506","authenticated-orcid":false,"given":"Anthony T","family":"Papenfuss","sequence":"additional","affiliation":[{"name":"The Walter and Eliza Hall Institute of Medical Research , Parkville, VIC 3052, Australia"},{"name":"Department of Medical Biology, University of Melbourne , Parkville, VIC 3052, Australia"},{"name":"Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre , East Melbourne, VIC 3002, Australia"},{"name":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3010, Australia"}]}],"member":"286","published-online":{"date-parts":[[2022,2,4]]},"reference":[{"key":"2023020109013311700_btac042-B1","doi-asserted-by":"crossref","first-page":"3240","DOI":"10.1038\/s41467-019-11146-4","article-title":"Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software","volume":"10","author":"Cameron","year":"2019","journal-title":"Nat. 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