Computational Approaches for Finding Long Insertions and Deletions with NGS Data

This chapter explains several aspects of the computational methods that call certain types of structural variation (SV), namely long insertions and deletions, using next-generation sequencing (NGS). It describes the main approaches from different categories, including the combined approaches. Each approach relies on some kind of signal contained in the reads that indicate the occurrence of SVs. Such signals are called as signatures of SVs. The chapter then introduces some ongoing projects that SV calling methods have been applied to. It provides a conclusion and discussion for future research directions. It provides an RD method called CNVnator (8), which calls copy number variations (CNV). The chapter focuses on describing computational tools that use combined signatures. The 1000 Genomes Project (1, 3) is the first large-scale project to sequence a large number of people in providing a comprehensive resource on human population genetic variation.