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Validation of Genomic Structural Variants Through Long Sequencing Technologies

  • Xuefang ZhaoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)

Abstract

Although numerous algorithms have been developed to identify large chromosomal rearrangements (i.e., genomic structural variants, SVs), there remains a dearth of approaches to evaluate their results. This is significant, as the accurate identification of SVs is still an outstanding problem whereby no single algorithm has been shown to be able to achieve high sensitivity and specificity across different classes of SVs. The method introduced in this chapter, VaPoR, is specifically designed to evaluate the accuracy of SV predictions using third-generation long sequences. This method uses a recurrence approach and collects direct evidence from raw reads thus avoiding computationally costly whole genome assembly. This chapter would describe in detail as how to apply this tool onto different data types.

Key words

VaPor Long read sequencing Structural Variants 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Center for Genomic Medicine at Massachusetts General HospitalBostonUSA

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