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Updated: Sep 6, 2025

Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise
Vinzenz May1, Leonard Koch2, Björn Fischer-Zirnsak2,3
1Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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 datasets and thus have the need to identify CNVs on their data to close the diagnostic gap.
Results:
In this article, we present our method clearCNV that addresses this need in two ways. First, it helps laboratories to properly assign datasets to enrichment kits. Based on homogeneous subsets of data, clearCNV identifies CNVs affecting the targeted regions. Using real-world datasets and validation, we show that our method is highly competitive with previous methods and preferable in terms of specificity.
Availability And Implementation:
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.
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