CNVfilteR

'CNVfilteR' is an R package to identify false positives in germline copy-number variant (CNV) calling tools used in next-generation sequencing (NGS) pipelines. The package utilizes single-nucleotide variant calls from germline NGS pipelines to identify false deletions and duplications. In evaluations with 13 CNV calling tools on three whole-genome sequencing and 541-panel samples, CNVfilteR demonstrated a significant decrease of up to 44.8% in false positives and a consistent increase in the F1-score. Integrating CNVfilteR into CNV calling pipelines can enhance overall performance by reducing false positives.

Topic

Sequencing;Workflows;Copy number variation

Detail

  • Operation: Copy number variation detection;Variant calling;Visualisation

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.16.0

  • Credit: Carlos III Health Institute co-funded by FEDER—a way to build Europe, the Government of Catalonia and CERCA.

  • Input: -

  • Output: -

  • Contact: Jose Marcos Moreno-Cabrera jpuntomarcos@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools.
  • Moreno-Cabrera JM, et al. CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools. CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools. 2021; 37:4227-4229. doi: 10.1093/bioinformatics/btab356
  • https://doi.org/10.1093/BIOINFORMATICS/BTAB356
  • PMID: 33983414
  • PMC: PMC9502136

Download and documentation

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