Document type
ArticleVersion
Published versionPublication date
Publication license
Please use this identifier to cite or link to this item: https://hdl.handle.net/2445/182882
CNVfilteR: an R/bioconductor package to identify false positives produced by germline NGS CNV detection tools.
Journal Title
Director/Tutor
Additional contribution
Journal ISSN
Volume Title
Abstract
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 3 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. Availability: CNVfilteR is released under Artistic-2.0 License. Source code and documentation are freely available at Bioconductor (http://www.bioconductor.org/packages/CNVfilteR). Supplementary information: Supplementary data are available at Bioinformatics online.
Related resource
Subject (English)
Citation
Citation
MORENO CABRERA, José Marcos, et al. CNVfilteR: an R/bioconductor package to identify false positives produced by germline NGS CNV detection tools. Bioinformatics. 2021. Vol. 37, num. 22, pags. 4227-4229. ISSN 1367-4803. [consulted: 14 of October of 2026]. Available at: https://hdl.handle.net/2445/182882