{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,26]],"date-time":"2025-05-26T15:46:23Z","timestamp":1748274383719,"version":"3.37.3"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004587","name":"Carlos III Health Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Government of Catalonia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015439","name":"CERCA","doi-asserted-by":"publisher","award":["PI16\/00563","PI19\/00553"],"award-info":[{"award-number":["PI16\/00563","PI19\/00553"]}],"id":[{"id":"10.13039\/100015439","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014139","name":"CIBERONC","doi-asserted-by":"publisher","award":["2017SGR1282","2017SGR496"],"award-info":[{"award-number":["2017SGR1282","2017SGR496"]}],"id":[{"id":"10.13039\/501100014139","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Germline copy-number variants (CNVs) are relevant mutations for multiple genetics fields, such as the study of hereditary diseases. However, available benchmarks show that all next-generation sequencing (NGS) CNV calling tools produce false positives. We developed CNVfilteR, an R package that uses the single-nucleotide variant calls usually obtained in germline NGS pipelines to identify those false positives. The package can detect both false deletions and false duplications. We evaluated CNVfilteR performance on callsets generated by 13 CNV calling tools on three whole-genome sequencing and 541 panel samples, showing a decrease of up to 44.8% in false positives and consistent F1-score increase. Using CNVfilteR to detect false-positive calls can improve the overall performance of existing CNV calling pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CNVfilteR is released under Artistic-2.0 License. Source code and documentation are freely available at Bioconductor (http:\/\/www.bioconductor.org\/packages\/CNVfilteR).<\/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\/btab356","type":"journal-article","created":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T19:22:57Z","timestamp":1620847377000},"page":"4227-4229","source":"Crossref","is-referenced-by-count":6,"title":["CNVfilteR: an R\/Bioconductor package to identify false positives produced by germline NGS CNV detection tools"],"prefix":"10.1093","volume":"37","author":[{"given":"Jos\u00e9 Marcos","family":"Moreno-Cabrera","sequence":"first","affiliation":[{"name":"Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti , Badalona, 08916 Barcelona, Spain"},{"name":"Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigaci\u00f3 Biom\u00e8dica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat , 08908 Barcelona, Spain"},{"name":"Instituto de Salud Carlos III, Centro de Investigaci\u00f3n Biom\u00e9dica en Red C\u00e1ncer (CIBERONC) , 28029 Madrid, Spain"}]},{"given":"Jes\u00fas","family":"del Valle","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigaci\u00f3 Biom\u00e8dica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat , 08908 Barcelona, Spain"},{"name":"Instituto de Salud Carlos III, Centro de Investigaci\u00f3n Biom\u00e9dica en Red C\u00e1ncer (CIBERONC) , 28029 Madrid, Spain"}]},{"given":"Elisabeth","family":"Castellanos","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti , Badalona, 08916 Barcelona, Spain"},{"name":"Clinical Genomics Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Germans Trias i Pujol University Hospital (HUGTiP), Campus Can Ruti , Badalona, 08916 Barcelona, Spain"}]},{"given":"Lidia","family":"Feliubadal\u00f3","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigaci\u00f3 Biom\u00e8dica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat , 08908 Barcelona, Spain"},{"name":"Instituto de Salud Carlos III, Centro de Investigaci\u00f3n Biom\u00e9dica en Red C\u00e1ncer (CIBERONC) , 28029 Madrid, Spain"}]},{"given":"Marta","family":"Pineda","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigaci\u00f3 Biom\u00e8dica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat , 08908 Barcelona, Spain"},{"name":"Instituto de Salud Carlos III, Centro de Investigaci\u00f3n Biom\u00e9dica en Red C\u00e1ncer (CIBERONC) , 28029 Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2895-9857","authenticated-orcid":false,"given":"Eduard","family":"Serra","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti , Badalona, 08916 Barcelona, Spain"},{"name":"Instituto de Salud Carlos III, Centro de Investigaci\u00f3n Biom\u00e9dica en Red C\u00e1ncer (CIBERONC) , 28029 Madrid, Spain"}]},{"given":"Gabriel","family":"Capell\u00e1","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigaci\u00f3 Biom\u00e8dica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat , 08908 Barcelona, Spain"},{"name":"Instituto de Salud Carlos III, Centro de Investigaci\u00f3n Biom\u00e9dica en Red C\u00e1ncer (CIBERONC) , 28029 Madrid, Spain"}]},{"given":"Conxi","family":"L\u00e1zaro","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, Institut d'Investigaci\u00f3 Biom\u00e8dica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat , 08908 Barcelona, Spain"},{"name":"Instituto de Salud Carlos III, Centro de Investigaci\u00f3n Biom\u00e9dica en Red C\u00e1ncer (CIBERONC) , 28029 Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8878-349X","authenticated-orcid":false,"given":"Bernat","family":"Gel","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti , Badalona, 08916 Barcelona, 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