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Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments
Xun Chen1, Guillaume Bourque2,3,4,5, Clément Goubert6,7,8
1Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan. xunchen85@gmail.com.
Abstract:
Transposable element (TE) insertions are a major source of structural variation in the human genome. Due to the repetitive nature and biological importance of TEs, many bioinformatic tools have been developed to identify and genotype TE insertion polymorphisms using high-throughput short-reads. In this chapter, we outline recently developed methods to characterize TE insertion polymorphisms in human populations. We also provide detailed protocols to tackle this question primarily using three software: MELT2, ERVcaller, and TypeREF.
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