Table 4.
Hapmap trio datasets results
| Datasets | Shape-IT | Phase v2.1 | Fastphase | Ishape | 2snp | Gerbil | PLEM | |||||||
| SER | Time | SER | Time | SER | Time | SER | Time | SER | Time | SER | Time | SER | Time | |
| CEU Size | 1.1 | 1.1 | 1.5 | 1.1 | 2.2 | 2.3 | 2.0 | |||||||
| 53 | 832 | 113 | 93 | < 1 | 50 | 10 | ||||||||
| YRI Size | 1.7 | 1.7 | 2.3 | 1.8 | 4.5 | 3.9 | 4.2 | |||||||
| 64 | 1,209 | 125 | 138 | < 1 | 131 | 10 | ||||||||
| CEU Density | 2.3 | 2.3 | 2.7 | 2.4 | 4.2 | 4.0 | 4.1 | |||||||
| 26 | 214 | 64 | 43 | < 1 | 5 | 6 | ||||||||
| YRI Density | 3.7 | 3.7 | 4.9 | 3.9 | 8.5 | 7.5 | 8.8 | |||||||
| 35 | 490 | 71 | 80 | < 1 | 9 | 5 | ||||||||
| CEU MAF | 1.1 | 1.1 | 1.2 | 1.2 | 2.0 | 2.1 | 1.7 | |||||||
| 19 | 104 | 71 | 22 | < 1 | 2 | 4 | ||||||||
| YRI MAF | 1.5 | 1.5 | 2.0 | 1.5 | 4.5 | 3.8 | 3.2 | |||||||
| 26 | 173 | 80 | 38 | < 1 | 4 | 4 | ||||||||
| CEU 50 illumina SNP | 6.3 | 6.3 | 7.2 | 6.6 | 10.7 | 9.2 | 12.2 | |||||||
| 51 | 1,214 | 60 | 161 | < 1 | 22 | 5 | ||||||||
| CEU 100 illumina SNP | 6.7 | 6.8 | 7.7 | 9.2 | 11.3 | 9.7 | N/A | |||||||
| 143 | 11,678 | 144 | 461 | < 1 | 254 | N/A | ||||||||
| CEU 200 illumina SNP | 7.2 | N/A | 8.0 | N/A | 11.5 | 9.9 | N/A | |||||||
| 372 | N/A | 198 | N/A | < 1 | 2,038 | N/A | ||||||||
N/A: software was unable to handle some of these datasets (errors or untracktable running times). Results of the various tested software on the HapMap trios datasets described in Table 1. For each software tested, the mean percentage of heterozygous markers incorrectly inferred (SER) is shown in the upper-left corner, and the mean running time in seconds is shown in the lower-right corner.