Table 5.
Comparison of SWER, MEC and runtimes for SDhaP and CPLEX on simulated diploid data with 5% error rate
| Data | Simulated data | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| SDhaP | CPLEX(optimal) | CPLEX(heuristic) | |||||||
| MEC | SWER | time | MEC | SWER | time | MEC | SWER | time | |
| l 103, c 10 | 535 | 0.04 | 1 | 518 | 0.036 | 811 | - | - | - |
| l 103, c 20 | 1042 | 0.007 | 4 | - | - | - | 1041 | 0.007 | 11393 |
| l 103, c 30 | 1583 | 0.003 | 4 | - | - | - | - | - | - |
| l 104, c 10 | 4971 | 0.099 | 14 | 4945 | 0.093 | 13800 | 7024 | 0.12 | 961 |
| l 104, c 20 | 9839 | 0.0370 | 41 | - | - | - | - | - | - |
| l 104, c 30 | 15310 | 0.0150 | 85 | - | - | - | - | - | - |
| l 105, c 10 | 51342 | 0.210 | 375 | - | - | - | - | - | - |
| l 105, c 20 | 102234 | 0.120 | 772 | - | - | - | - | - | - |
| l 105, c 30 | 157234 | 0.030 | 1517 | - | - | - | - | - | - |
MEC, SWER and running times (in seconds) for SDhaP, RefHap, HAPCUT and HapTree algorithms for simulated data of different lengths (l) and with different coverages (c). The data contains a fixed 5% fraction of genotyping errors. SDhaP is more accurate in terms of MEC and SWER and faster by almost an order of magnitude compared to other schemes for longer blocks.