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R package to remove false positives of CNV calling tools by using SNV calls

Many tools for germline copy number variant (CNV) detectionfrom NGS data have been developed. Usually, these tools weredesigned for different input data like WGS, WES orpanel data, and their performance may depend on the CNV size. Availablebenchmarks show that all these tools obtain false positives, sometimesreaching a very high number of them.

With the aim of reducing the number of false positives,CNVfilteR identifies thosegermline CNVs that can be discarded. This task is performed by using thegermline single nucleotide variant (SNV) calls that are usuallyobtained in common NGS pipelines. As VCF field interpretation is keywhen working with these files, CNVfilteR specifically supportsVCFs produced by VarScan2, Strelka/Strelka2, freeBayes, HaplotypeCaller,UnifiedGenotyper and Torrent Variant Caller. Additionally, results can beplotted using the functions provided by the R/Bioconductor packageskaryoploteR andCopyNumberPlots.

Documentation (vignette anduser manual) are available at theCNVfilteRBioconductor site, allow with instructions to install it.

CNVfilteR was developed by José Marcos Moreno-Cabrera and Bernat Gel. For citations,please refer to theBioinformatics paper:

José Marcos Moreno-Cabrera, Jesús del Valle, Elisabeth Castellanos, Lidia Feliubadaló, Marta Pineda, Eduard Serra, Gabriel Capellá, Conxi Lázaro, Bernat Gel,CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools, Bioinformatics, 2021;, btab356,https://doi.org/10.1093/bioinformatics/btab356