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Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

By David Jakubosky, Erin N. Smith, Matteo D'Antonio, Marc Jan Bonder, William W Young Greenwald, Agnieszka D’Antonio-Chronowska, Hiroko Matsui, i2QTL Consortium, HipSci Consortium, Oliver Stegle, Stephen B. Montgomery, Christopher DeBoever, Kelly A Frazer

Posted 24 Jul 2019
bioRxiv DOI: 10.1101/713198 (published DOI: 10.1038/s41467-020-16481-5)

Structural variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assembled a set of 719 deep whole genome sequencing (WGS) samples (mean 42x) from 477 distinct individuals which we used to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We used 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and developed a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.

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