Table 4. .
Timing Results
| Time(s per Marker) |
||||||||||
| Low-Density Simulateda |
High-Density Simulateda |
Affymetrix 500K WTCCCb |
||||||||
| Method | Small | Medium | Large | Small | Medium | Large | Small | Medium | Large | Xc |
| Beagled: | ||||||||||
| R=25 | .07 | .58 | 12.95 | .07 | 1.05 | 16.42 | .07 | .88 | 6.50 | .34 |
| R=4 | .04 | .14 | 4.13 | .03 | .31 | 9.62 | .03 | .19 | 1.14 | .11 |
| R=1 | .02 | .10 | 1.80 | .01 | .13 | 4.55 | .02 | .09 | .34 | .07 |
| fastPHASEe: | ||||||||||
| K=20 | 3.03 | 32.33 | 150.69 | 3.49 | 30.25 | 150.60 | 3.02 | 29.74 | 89.12 | 22.00 |
| K=10 | .89 | 9.63 | 44.67 | 1.14 | 11.74 | 44.59 | .89 | 8.92 | 26.67 | 6.43 |
| HaploRec-S | .60 | 6.26 | 27.93 | 1.23 | 8.02 | 22.63 | .48 | 13.78 | 57.76 | 5.02 |
| HaploRec-VMM | .28 | 3.50 | 33.98 | .25 | 6.07 | 17.72 | .28 | 7.63 | 34.04 | 1.15 |
| HAP | 1.75 | 23.31 | 733.02 | .45 | 41.49 | 613.13 | .38 | 15.79 | 95.36 | 4.83 |
| 2SNP | .01 | .07 | 1.02 | .00 | .09 | 1.49 | .01 | .17 | 1.20 | .04 |
a
Parameters for selection of tag SNPs for 1 Mb of simulated data were chosen to obtain approximate densities of 1 SNP per 10 kb (low density) or 1 SNP per 3 kb (high density). For each density, three sample sizes were considered: 100 (small), 1,000 (medium), and 5,000 (large) individuals.
b
For the WTCCC data, sets of 200 consecutive markers were used. Three sample sizes were considered: 100 (small), 1,000 (medium), and 3,002 (large) individuals.
c
“X” represents 732 X-chromosome pairs constructed from male X-chromosome data.
d
Beagle results are given for R=1, R=4, and R=25 samples per individual.
e
fastPHASE results are given for K=10 and K=20 clusters per individual.