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Updated: Nov 5, 2025
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools
José Marcos Moreno-Cabrera1,2,3, Jesús Del Valle2,3, Elisabeth Castellanos1,4
1Hereditary 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.
Summary:
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.
Availability And Implementation:
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.
