ABSTRACT
This chapter studies methods for calling variations that cover longer regions, which are known as structural variations (SVs). SVs are large-scale changes in our genome, often more than 50 nucleotides. The simple SVs can be classified into balanced SVs and unbalanced SVs. Balanced SVs just rearrange our genomes. They include reversal, transposition and translocation. Unbalanced SVs alternate the number of copies of some deoxyribonucleic acid segments, which is usually referred to as copy number variation (CNV). Complex SVs are formed by combining a number of simple SVs. The chapter describes how SVs are formed and covers the clinical effects of SVs. It details different wet-lab techniques to determine SVs and discusses the computation techniques for calling CNVs. The chapter also describes different verification methods for candidate SVs, including validation by the unused paired-end read information, validation by assembling the paired-end reads, statistical analysis for filtering the low-confidence SVs, and verification using biological features.
