ABSTRACT
This chapter briefly reviews the genetics of structural variation, provides an overview of the major algorithmic approaches that have been developed to characterize structural variation in WES/WGS data. In human genetics, Array-comparative genomic hybridization (CGH) is a commonly used screening investigation to investigate nearly the entire genome for copy number variants (CNVs) in an untargeted fashion, and is used in the workup of intellectual disability or developmental delay of unknown cause, congenital malformations or facial dysmorphism, and autism. Array-CGH still remains the gold standard for the diagnostic investigation of structural variation in these cases. The chapter deals with presentations of the CoNIFE method for separated value (SV) detection in WES data as well as CNVnator and DELLY for SV detection in WGS data. CoNIFER uses Singular Value Decomposition (SVD) to "denoise" the WES data and enable accurate CNV calling.
