Genotype Representation Graphs: Enabling Efficient Analysis of Biobank-Scale Data.

ABSTRACT: Computational analysis of a large number of genomes requires a data structure that can represent the dataset compactly while also enabling efficient operations on variants and samples. Current practice is to store large-scale genetic polymorphism data using tabular data structures and file formats, where rows and columns represent samples and genetic variants. However, encoding genetic data in such formats has become unsustainable. For example, the UK Biobank polymorphism data of 200,000 phased whole genomes has exceeded 350 terabytes (TB) in Variant Call Format (VCF), cumbersome and inefficient to work with. To mitigate the computational burden, we introduce the Genotype Representation Graph (GRG), an extremely compact data structure to losslessly present phased whole-genome polymorphisms

SUBMITTER: DeHaas D 

PROVIDER: S-EPMC11071416 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature