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

Item Type:Article
Title:ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise
Creators Name:May, V. and Koch, L. and Fischer-Zirnsak, B. and Horn, D. and Gehle, P. and Kornak, U. and Beule, D. and Holtgrewe, M.
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}}.
Keywords:DNA Copy Number Variations, Exons, High-Throughput Nucleotide Sequencing, Software
Publisher:Oxford University Press
Page Range:3871-3876
Date:15 August 2022
Official Publication:https://doi.org/10.1093/bioinformatics/btac418
PubMed:View item in PubMed

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