Generating and implementing a structural variation graph genome

Abstract

This disclosure describes methods, non-transitory computer readable media, and systems that can generate a structural variation graph genome with alternate contiguous sequences representing structural variant haplotypes. For instance, the disclosed systems can identify candidate structural variants that satisfy an occurrence threshold within a genomic sample database. From among the candidate structural variants, the systems select structural variant haplotypes based on one or both of the structural variant haplotypes satisfying a relative haplotype frequency and finding flanking variants adjacent to particular structural variant haplotypes. The systems can likewise select reference haplotypes corresponding to the selected structural variant haplotypes from a reference genome. Based on the selected haplotypes, the disclosed systems generate a structural variation graph genome comprising both alternate contiguous sequences representing the structural variant haplotypes and reference sequences representing the reference haplotypes.

Dependencies are inferred from the claim text.