ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise

Abstract Motivation While the identification of small variants in panel sequencing data can be considered a solved problem, the identification of larger, multi-exon copy number variants (CNVs) still poses a considerable challenge. Thus, CNV calling has not been established in all laboratories performing panel sequencing. At the same time such laboratories have accumulated large data sets and thus have the need to identify copy number variants on their data to close the diagnostic gap. Results In this manuscript we present our method clearCNV that addresses this need in two ways. First, it helps laboratories to properly assign data sets to enrichment kits. Based on homogeneous subsets of data, clearCNV identifies CNVs affecting the targeted regions. Using real-world data sets and validation, we show that our method is highly competitive with previous methods and preferable in terms of specificity. Availability The software is available for free under a permissible license at {{https://github.com/bihealth/clear-cnv}} Supplementary information Supplementary data are available at Bioinformatics online.