Introduction

CNVfilteR identifies those copy number variants (CNVs) that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines. Many tools for germline CNV detection from NGS data have been developed. Usually, these tools were designed for different input data like WGS, WES or panel data, and their performance may depend on the CNV size. Available benchmarks show that all these tools obtain false positives, sometimes reaching a very high number of them.

With the aim of reducing the number of false positives, CNVfilteR identifies those germline CNVs that can be discarded. This task is performed by using the germline SNV calls that are usually obtained in common NGS pipelines. As VCF field interpretation is key when working with these files, CNVfilteR specifically supports VCFs produced by VarScan2, Strelka/Strelka2, freeBayes, HaplotypeCaller, UnifiedGenotyper and Torrent Variant Caller. Additionally, results can be plotted using the functions provided by the R/Bioconductor packages karyoploteR and CopyNumberPlots.

For more information, visit the CNVfilteR official website.

Programming language: R

Brief description: identifies those CNVs that can be discarded by using the SNV calls that are usually obtained in common NGS pipelines.

Open source license: Artistic License 2.0