Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats

David Jakubosky, Erin N. Smith, Matteo D’Antonio, Marc Bonder, William W. Young Greenwald, Agnieszka D’Antonio-Chronowska, Hiroko Matsui, Oliver Stegle, Stephen B. Montgomery, Christopher DeBoever and Kelly A. Frazer ()
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David Jakubosky: University of California San Diego
Erin N. Smith: University of California San Diego
Matteo D’Antonio: University of California San Diego
Marc Bonder: European Bioinformatics Institute
William W. Young Greenwald: University of California San Diego
Agnieszka D’Antonio-Chronowska: University of California San Diego
Hiroko Matsui: University of California San Diego
Oliver Stegle: European Bioinformatics Institute
Stephen B. Montgomery: Stanford University
Christopher DeBoever: University of California San Diego
Kelly A. Frazer: University of California San Diego

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: Abstract 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 assemble a set of 719 deep whole genome sequencing (WGS) samples (mean 42×) from 477 distinct individuals which we use to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We use 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and develop a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.

Date: 2020
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DOI: 10.1038/s41467-020-16481-5

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