# Copy Number Variation: Methods and Clinical Applications
## 2 Methods of CNV Detection
### Methods of Molecular Biology
When considering in silico tools to extract CNV genotype information from generated data, nearly all of the available methods have their dedicated commercial tools, from cytogenetic karyotyping, through MLPA, up to aCGH. The bioinformatic tools for processing MPS data are, however, still under intensive development and diversification (Table 1). While both 2 GS and 3 GS are technically capable of detecting CNVs in a wide range of length, not each size is identifiable using the same bioinformatics pipeline and different variants may require differently suited tools [50]. To identify smaller structural variations spanning several nucleotides, conventional variant callers, such as the GATK HaplotypeCaller [51], are generally suitable, while large CNVs exceeding read lengths are typically identified based on a disproportion of sequenced reads from the genomic region of a particular CNV [52]. In conclusion, since each CNV detecting method has its advantages and limitations, the choice for an appropriate technique depends on the application, required resolution, available lab equipment, workload, and budget. \begin{table}
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**Tool** & **Description** & **Operating System** & **Availability** & **Reference** \\ \hline \multirow{4}{*}{Wisecondor} & A tool for detecting small sub-chromosomal and chromosomal genetic CNV alterations in fetal DNA using low coverage sequencing of maternal cfDNA. It allows less-invasive detection of chromosomal CNV changes at a resolution comparable to conventional cytogenetic analysis. Moreover, no re-sequence healthy samples are needed for normalization. & Mac OS X Linux & Free for non-commercial use & [53; 54] \\ \hline \multirow{4}{*}{ExomeCNV} & ExomeCNV is based on an algorithm using statistics of sequence coverage and B-allele frequencies for CNV and loss of heterozygosity significantly by mapping short sequence reads. & MS Windows Mac OS X Linux & Free-software license & [55] \\  & ExomeCNV was the first tool implemented to detect CNVs from WES data. & MS Windows Mac OS X Linux & Free-software license & [56] \\ \hline \multirow{4}{*}{SAvvyCNV} & A tool that can generate high-quality DNA copy number profiles using off-target reads from targeted sequencing data. In addition, Copywrite allows extracting accurate copy number information without a reference. & MS Windows Mac OS X Linux & Free-software license & [57] \\ \hline \multirow{4}{*}{DECon} & A fast and accurate tool for exon CNV detection from whole exons in targeted panel analysis, capable of detecting small intra-exor variants. It provides quality checks and visualization to make it suitable for clinical use. & MS Windows Mac OS X Linux & Freely available & [58] \\ \hline \multirow{4}{*}{CNVkit} & A software toolkit for detection, analysis, and visualization of CNVs, able to estimate CNVs and alterations genome-wide from high-throughput sequencing data. It implements a pipeline for CNV detection that takes advantage of both on- and off-target reads and applies a series of corrections to improve copy number calling accuracy. & Mac OS X Linux & Free software license & [59] \\ \cline{1-1} \cline{2-4}  & & & & \\ \cline{1-1} \cline{2-4}  & & & & \\ \cline{1-1} \cline{2-4}  & & & & \\ \cline{1-1} \cline{2-4}  & & & & \\ \cline{1-1} \cline{2-4}  & & & & \\ \cline{1-1} \cline{2-4}  & & & & \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Bioinformatic tools for detection of CNVs from next generation sequencing-based genomic data. Several tools are capable of detection and annotation of CNVs at the same time (e.g., iCopyDAV, SG-ADVISER-CNV, DeAnnCNV), so they are listed in the next table. WES (whole-exome sequencing); WGS (whole-genome sequencing).