{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T20:01:11Z","timestamp":1762459271837},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Identification of structural variants (SVs) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation.<\/jats:p>\n               <jats:p>Results: Simulations using RAPTR-SV and other, similar algorithms for SV detection revealed that RAPTR-SV had superior sensitivity and precision, as it recovered 66.4% of simulated tandem duplications with a precision of 99.2%. When compared with calls made by Delly and LUMPY on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications, as it identified 2-fold more duplications than Delly, while making \u223c85% fewer duplication predictions.<\/jats:p>\n               <jats:p>Availability and implementation: RAPTR-SV is written in Java and uses new features in the collections framework in the latest release of the Java version 8 language specifications. A compiled version of the software, instructions for usage and test results files are available on the GitHub repository page: https:\/\/github.com\/njdbickhart\/RAPTR-SV.<\/jats:p>\n               <jats:p>Contact: derek.bickhart@ars.usda.gov<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv086","type":"journal-article","created":{"date-parts":[[2015,2,17]],"date-time":"2015-02-17T01:13:30Z","timestamp":1424135610000},"page":"2084-2090","source":"Crossref","is-referenced-by-count":15,"title":["RAPTR-SV: a hybrid method for the detection of structural variants"],"prefix":"10.1093","volume":"31","author":[{"given":"Derek M.","family":"Bickhart","sequence":"first","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State University, Ames, IA 50011, USA"}]},{"given":"Jana L.","family":"Hutchison","sequence":"additional","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State University, Ames, IA 50011, USA"}]},{"given":"Lingyang","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State University, Ames, IA 50011, USA"}]},{"given":"Robert D.","family":"Schnabel","sequence":"additional","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State University, Ames, IA 50011, USA"}]},{"given":"Jeremy F.","family":"Taylor","sequence":"additional","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State University, Ames, IA 50011, USA"}]},{"given":"James M.","family":"Reecy","sequence":"additional","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State University, Ames, IA 50011, USA"}]},{"given":"Steven","family":"Schroeder","sequence":"additional","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State University, Ames, IA 50011, USA"}]},{"given":"Curt P.","family":"Van Tassell","sequence":"additional","affiliation":[{"name":"1 Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, 2Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, 3Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and 4Department of Animal Science, Iowa State 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