Abstract

Variant affecting more than 50 nucleotides, or structural variants, can have important functional impacts. They unfortunately tend to be understudied because of technical challenges hindering their detection. I will present two approaches to integrate those variants in genomic studies. The first uses pangenomes as augmented reference genome containing common variants (including structural variants). With this more complete reference, short sequencing reads are better analyzed, resulting in a larger number of structural variants that can be genotyped accurately. The second approach uses cost-efficient long read sequencing technology, such as Oxford Nanopore, to infer phased variants at unprecedented resolution.