Figure 4.

Memory Use and Computation Time for Beagle v.4.1 for Millions of Reference Samples

Beagle’s memory requirements and computation time for imputing 10 Mb of simulated sequence data from binary reference files having one million to five million reference samples, each with 1,294,053 markers. The simulated imputation target was 1,000 individuals genotyped on a 1M SNP array (3,333 markers in the 10 Mb region). CPU time includes the sum of the computation time consumed by each computational thread. All Beagle analyses used 12 computational threads. The wall clock computation time required to prepare each binary reference file was approximately four to five times greater than the wall clock imputation time reported in this figure.