CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools

• DOI: 10.1093/bioinformatics/btab356
• Publication Date: 2021-05-12T19:22:57Z
• Authors: José Marcos Moren...; Jesús del Valle; Elisabeth Castell...; Lidia Feliubadaló; Marta Pineda; Eduard Serra; Gabriel Capellá; Conxi Lázaro; Bernat Gel
• Keywords: Bioconductor; Copy number analysis; R package

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 uses single-nucleotide variant calls usually obtained in germline NGS pipelines to identify those The can detect both deletions and duplications. evaluated CNVfilteR performance on callsets generated by 13 three whole-genome 541 panel samples, showing a decrease up 44.8% positives consistent F1-score increase. Using false-positive improve overall existing pipelines.CNVfilteR is released under Artistic-2.0 License. Source code documentation freely at Bioconductor (http://www.bioconductor.org/packages/CNVfilteR).Supplementary data Bioinformatics online.