We developed a new BGEN file format (v1.2; http://www.well.ox.ac.uk/~gav/bgen_format/bgen_format.html) and software library (BGEN; https://bitbucket.org/gavinband/bgen) to provide improved data compression, the ability to store phased haplotype data and random access to the data via use of a separate index file. Using this new format, the full imputed files require 2.1 Tb of file space. A new program (BGENIE; https://jmarchini.org/software) was built using the BGEN library to carry out fast multi-trait GWAS and phenome-wide association studies28 (see Supplementary Information).
