README.md

In jpuntomarcos/CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

CNVfilteR

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

Introduction

Many tools for germline copy number variant (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 single nucleotide variant (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.

How to use it

Documentation (vignette and user manual) are available at the CNVfilteR Bioconductor site, allow with instructions to install it.

Citation

CNVfilteR was developed by José Marcos Moreno-Cabrera and Bernat Gel. For citations, please refer to the Bioinformatics 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

jpuntomarcos/CNVfilteR documentation built on Oct. 6, 2023, 12:37 a.m.