{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T07:20:25Z","timestamp":1775978425803,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1490,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs.<\/jats:p>\n               <jats:p>Results: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity.<\/jats:p>\n               <jats:p>Availability: DELLY is available at www.korbel.embl.de\/software.html<\/jats:p>\n               <jats:p>Contact: \u00a0tobias.rausch@embl.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts378","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T20:35:22Z","timestamp":1347050122000},"page":"i333-i339","source":"Crossref","is-referenced-by-count":2251,"title":["DELLY: structural variant discovery by integrated paired-end and split-read analysis"],"prefix":"10.1093","volume":"28","author":[{"given":"Tobias","family":"Rausch","sequence":"first","affiliation":[{"name":"1 European Molecular Biology Laboratory (EMBL), Genome Biology, Meyerhofstr. 1, 69117 Heidelberg, Germany"},{"name":"3 European Molecular Biology Laboratory (EMBL), Core Facilities and Services, Meyerhofstr. 1, 69117 Heidelberg, Germany"}]},{"given":"Thomas","family":"Zichner","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory (EMBL), Genome Biology, Meyerhofstr. 1, 69117 Heidelberg, Germany"}]},{"given":"Andreas","family":"Schlattl","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory (EMBL), Genome Biology, Meyerhofstr. 1, 69117 Heidelberg, Germany"}]},{"given":"Adrian M.","family":"St\u00fctz","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory (EMBL), Genome Biology, Meyerhofstr. 1, 69117 Heidelberg, Germany"}]},{"given":"Vladimir","family":"Benes","sequence":"additional","affiliation":[{"name":"3 European Molecular Biology Laboratory (EMBL), Core Facilities and Services, Meyerhofstr. 1, 69117 Heidelberg, Germany"}]},{"given":"Jan O.","family":"Korbel","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory (EMBL), Genome Biology, Meyerhofstr. 1, 69117 Heidelberg, Germany"},{"name":"2 EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012512590951000_B1","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","author":"1000 Genomes Project Consortium","year":"2010","journal-title":"Nature"},{"key":"2023012512590951000_B2","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1093\/bioinformatics\/btq713","article-title":"Age: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision","volume":"27","author":"Abyzov","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512590951000_B3","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res."},{"key":"2023012512590951000_B4","first-page":"9","article-title":"Realigner: a program for refining DNA sequence multi-alignments","volume-title":"Proc. 1st Annual International Conference on Research in Computational Molecular Biology","author":"Anson","year":"1997"},{"key":"2023012512590951000_B5","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","article-title":"BamTools: a C++ API and toolkit for analyzing and managing BAM files","volume":"27","author":"Barnett","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512590951000_B6","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/ng.128","article-title":"Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing","volume":"40","author":"Campbell","year":"2008","journal-title":"Nat. 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