How long does imputation take?
The following factors/parameters affect computational time: • m, # of genotyped markers (number of markers in .dat file) • n, # of individuals • h, # of reference haplotypes (determined by –greedy or states, by default, h = 2*number diploid individuals – 2 + number_haplotypes) • r, # of rounds (-r or –rounds, –mle corresponds to 1-2 rounds) Computational time increases linearly with m, n, r and quadratically with h. On our Xeon 3.0GHz machine, imputation with m=25K, n=250, h=120, and r=100 takes ~20 hours (25000*250*120^2*100/4.5/10^11). If you have a larger number of individuals to impute (e.g., > 1,000), we recommend a 2-step imputation manner http://genome.sph.umich.edu/wiki/MaCH_FAQ#Why_and_how_to_perform_a_2-step_imputation.3F.
