Table 2

Timing results from simulations of extreme amounts of missing data

Total % missing

Simulation probability

Runtime

Slowdown

Speedup vs. Merlin


5%

3.83%

3.274 s

5.21%

306×

10%

8.83%

3.564 s

14.5%

281×

20%

18.8%

4.567 s

46.8%

220×

30%

28.8%

6.897 s

122%

145×

40%

38.8%

11.36 s

265%

88.5×

50%

48.8%

36.38 s

1070%

27.6×


Hapi's runtime performance for haplotyping the dataset discussed in Results in the presence of various total proportions of missing data. Because this dataset contains 1.17% missing data already, we dropped genotypes according to the indicated probabilities in order to obtain the total overall proportions of missing data. The table lists the runtime, percentage slowdown compared to running Hapi on the unmodified dataset, and the speedup compared to running Merlin on the unmodified dataset.

Williams et al. Genome Biology 2010 11:R108   doi:10.1186/gb-2010-11-10-r108

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