Supplementary Figure 1: The walltimes when splitting up the data set.

The walltimes per job for MaCH (a, c, e) and minimac (b, d, f) for various ways of splitting up the data set. The walltime is the time as measured by a clock on the wall (CPU time, disk writing etcetera) required to impute the target set. The walltime per job for running MaCH fits the linear regression models t=8.6 + 1.13n (Figure a), t=86.49 + 270.02n (Figure c) and t=1568.3 + 2.7n (Figure e). The walltime per job for running minimac fits the linear regression model t=33.8 + 0.13n (split before MaCH (blue circles)), t=50.2 + 0.10n (split after MaCH (green squares)) (Figure b), t=688.6 + 3.29n (Figure d) and t=687.7 + 0.02n (Figure f). t is the walltime in minutes and n the number of samples (a, b), the size of the chunks in Mb (c, d) and the percentage of overlap (e, f). The percentage overlap is 10% in Figure c and d and the chunk size is 5Mb in Figure e and f.