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However, the accurate detection of CNVs from targeted next-generation sequencing (NGS) gene panel data remains a challenging task. Several tools for calling CNVs within this context have been published to date, but the available benchmarks suffer from limitations, including testing on simulated data, testing on small datasets, and testing a small subset of published tools. In this work, we conducted a comprehensive benchmarking of 12 tools (Atlas-CNV, ClearCNV, ClinCNV, CNVkit, Cobalt, CODEX2, CoNVaDING, DECoN, ExomeDepth, GATK-gCNV, panelcn.MOPS, VisCap) on four validated gene panel datasets using their default parameters. We also assessed the impact of modifying 107 tool parameters and identified 13 parameter values that we suggest using to improve the tool F1 score. A total of 66 tool pair combinations were also evaluated to produce better meta-callers. Furthermore, we developed CNVbenchmarker2, a framework to help users perform their own evaluations. Our results indicated that in terms of F1 score, ClinCNV and GATK-gCNV were the best CNV callers. Regarding sensitivity, GATK-gCNV also exhibited particularly high performance. The results presented here provide an evaluation of the current state of the art in germline CNV detection from gene panel data and can be used as a reference resource when using any of the tools.<\/jats:p>","DOI":"10.1093\/bib\/bbae645","type":"journal-article","created":{"date-parts":[[2024,12,13]],"date-time":"2024-12-13T03:47:56Z","timestamp":1734061676000},"source":"Crossref","is-referenced-by-count":6,"title":["Detection of germline CNVs from gene panel data: benchmarking the state of the art"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8396-8284","authenticated-orcid":false,"given":"Elisabet","family":"Munt\u00e9","sequence":"first","affiliation":[{"name":"Hereditary Cancer Program , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge - IDIBELL-ONCOBELL , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Doctoral Programme in Biomedicine, University of Barcelona (UB) , Casanova 143, 08036 Barcelona,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1171-0588","authenticated-orcid":false,"given":"Carla","family":"Roca","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge - IDIBELL-ONCOBELL , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Doctoral Programme in Biomedicine, University of Barcelona (UB) , Casanova 143, 08036 Barcelona,","place":["Spain"]}]},{"given":"Jes\u00fas","family":"Del Valle","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge - IDIBELL-ONCOBELL , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de C\u00e1ncer (CIBERONC), Instituto de Salud Carlos III , Monforte de Lemos 5, 28029 Madrid,","place":["Spain"]}]},{"given":"Lidia","family":"Feliubadal\u00f3","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge - IDIBELL-ONCOBELL , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de C\u00e1ncer (CIBERONC), Instituto de Salud Carlos III , Monforte de Lemos 5, 28029 Madrid,","place":["Spain"]}]},{"given":"Marta","family":"Pineda","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge - IDIBELL-ONCOBELL , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de C\u00e1ncer (CIBERONC), Instituto de Salud Carlos III , Monforte de Lemos 5, 28029 Madrid,","place":["Spain"]}]},{"given":"Bernat","family":"Gel","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP) , Can Ruti Campus, Cam\u00ed de les Escoles s\/n, 08916 Badalona, Barcelona,","place":["Spain"]}]},{"given":"Elisabeth","family":"Castellanos","sequence":"additional","affiliation":[{"name":"Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP) , Can Ruti Campus, Cam\u00ed de les Escoles s\/n, Badalona, Barcelona,","place":["Spain"]},{"name":"Genetics Department, Germans Trias i Pujol University Hospital (HUGTiP) , Can Ruti Campus, Carretera de Canyet s\/n, 08916 Badalona, Barcelona,","place":["Spain"]}]},{"given":"Barbara","family":"Rivera","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge - IDIBELL-ONCOBELL , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L\u2019Hospitalet de Llobregat,","place":["Spain"]},{"name":"Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital , 3755 Chemin de la C\u00f4te-Sainte-Catherine, Montreal, QC,","place":["Canada"]},{"name":"Gerald Bronfman Department of Oncology, McGill University , 5100 de Maisonneuve Blvd. West, Suite 720 Montreal, QC,","place":["Canada"]}]},{"given":"David","family":"Cordero","sequence":"additional","affiliation":[{"name":"Unit of Bioinformatics for Precision Oncology (UBOP), Catalan Institute of Oncology , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]},{"name":"Preclinical and Experimental Research in Thoracic Tumors (PReTT) , ONCOBELL Program, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge (IDIBELL) , ONCOBELL Program, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]},{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red de Epidemiolog\u00eda y Salud P\u00fablica (CIBERESP), Instituto de Salud Carlos III , Monforte de Lemos 5, 28029 Madrid,","place":["Spain"]}]},{"given":"V\u00edctor","family":"Moreno","sequence":"additional","affiliation":[{"name":"Consorcio de Investigaci\u00f3n Biom\u00e9dica en Red de Epidemiolog\u00eda y Salud P\u00fablica (CIBERESP), Instituto de Salud Carlos III , Monforte de Lemos 5, 28029 Madrid,","place":["Spain"]},{"name":"Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]},{"name":"Colorectal Cancer Group , ONCOBELL Program, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]},{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica de Bellvitge (IDIBELL) , ONCOBELL Program, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]},{"name":"Department of Clinical Sciences , Faculty of Medicine and Health Sciences, Universitat de Barcelona Institute of Complex Systems (UBICS), , Freixa Llarga s\/n, 08907 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]},{"name":"University of Barcelona (UB) , Faculty of Medicine and Health Sciences, Universitat de Barcelona Institute of Complex Systems (UBICS), , Freixa Llarga s\/n, 08907 L'Hospitalet de Llobregat, Barcelona,","place":["Spain"]}]},{"given":"Conxi","family":"L\u00e1zaro","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program , Catalan Institute of Oncology, , Avinguda de la Granvia de l\u2019Hospitalet, 199, 08908 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