BGEN: a binary file format for imputed genotype and haplotype data

Abstract

The impact of modern technology on genetic epidemiology has been significant, with studies comprising millions of individuals assessed at tens of millions of genetic variants now becoming common. Studies on this scale provide logistical and analytic challenges starting with the issue of efficiently storing, transmitting, and accessing underlying data. Here we present a binary file format (the BGEN format) that can store both directly-typed and statistically imputed genotype data, and achieves substantial space savings by data compression and the use of an efficient representation for probabilities. We investigate the properties of this format using imputed data from the UK BiLEVE study, demonstrating both storage efficiency, and fast data loading performance on the order of hundreds of millions of imputed genotypes per second. To make using BGEN as easy as possible, we provide a detailed specification and a freely available reference implementation, and we leverage this by developing additional tools including an indexing tool (bgenix) and an R package (rbgen) that permits loading of BGEN-encoded data into the R statistical programming environment. The UK Biobank is one of a number of projects that have used BGEN for release of imputed data, and we expect the format to continue to be widely implemented and used.