VariantStore: an index for large-scale genomic variant search

Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic variants from multiple samples using a variation graph and enables variant queries across any sample-specific coordinate system. We show the scalability of VariantStore by indexing genomic variants from the TCGA project in 4 h and the 1000 Genomes project in 3 h. Querying for variants in a gene takes between 0.002 and 3 seconds using memory only 10% of the size of the full representation.

Automated summary

VariantStore efficiently indexes genomic variants from multiple samples using a variation graph, enabling variant queries across different sample-specific coordinate systems. It demonstrates scalability by indexing genomic variants from the TCGA and 1000 Genomes projects in a short amount of time, with queries for gene variants taking between 0.002 and 3 seconds, using only 10% of the full representation's memory.