The availability of long reads is revolutionizing studies of structural
variants (SVs). However, because SVs vary across individuals and are
discovered through imprecise read technologies and methods, they can be
difficult to compare. Addressing this, we present Jasmine and Iris (
https://github.com/mkirsche/Jasmine/ ), for fast and accurate SV
refinement, comparison and population analysis. Using an SV proximity
graph, Jasmine outperforms six widely used comparison methods, including
reducing the rate of Mendelian discordance in trio datasets by more than
fivefold, and reveals a set of high-confidence de novo SVs confirmed by
multiple technologies. We also present a unified callset of 122,813 SVs and
82,379 indels from 31 samples of diverse ancestry sequenced with long
reads. We genotype these variants in 1,317 samples from the 1000 Genomes
Project and the Genotype-Tissue Expression project with DNA and
RNA-sequencing data and assess their widespread impact on gene expression,
including within medically relevant genes.
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