Table 2 performance of the various algorithms on the GH1 and APOE datasets
From: ISHAPE: new rapid and accurate software for haplotyping
2A. GH1 dataset | ||||||||
|---|---|---|---|---|---|---|---|---|
Soft | MD | IF | IER | Time (sec.) | MD | IF | IER | Time (sec.) |
Ishape1 | 0% | 0.927 +/- 0.001 | 0.119 +/- 0.001 | 0.9 | 5% | 0.915 +/- 0.002 | 0.164 +/- 0.004 | 1.7 |
Ishape2 | 0.937 +/- 0.001 | 0.103 +/- 0.001 | 9.2 | 0.927 +/- 0.002 | 0.147 +/- 0.004 | 11.5 | ||
Phase2.1 | 0.937 +/- 0.001 | 0.103 +/- 0.001 | 62.9 | 0.924 +/- 0.002 | 0.148 +/- 0.004 | 71.4 | ||
Phase1.0 | 0.926 +/- 0.002 | 0.119 +/- 0.002 | 15.6 | 0.915 +/- 0.003 | 0.164 +/- 0.005 | 26.0 | ||
FastPhase | 0.928 +/- 0.001 | 0.105 +/- 0.001 | 139.1 | 0.920 +/- 0.002 | 0.170 +/- 0.004 | 138.9 | ||
PL-EM | 0.915 +/- 0.001 | 0.116 +/- 0.000 | 0.3 | 0.890 +/- 0.003 | 0.171 +/- 0.003 | 3.2 | ||
2snp | NA | 0.157 +/- 0.000 | < 0.1 | NA | 0.214 +/- 0.002 | < 0.1 | ||
Ishape1 | 2% | 0.922 +/- 0.001 | 0.137 +/- 0.003 | 1.2 | 10% | 0.905 +/- 0.002 | 0.208 +/- 0.004 | 2.8 |
Ishape2 | 0.933 +/- 0.001 | 0.120 +/- 0.002 | 10.6 | 0.916 +/- 0.002 | 0.195 +/- 0.005 | 14.6 | ||
Phase2.1 | 0.931 +/- 0.001 | 0.122 +/- 0.003 | 64.6 | 0.914 +/- 0.002 | 0.196 +/- 0.005 | 82.5 | ||
Phase1.0 | 0.921 +/- 0.002 | 0.138 +/- 0.003 | 20.7 | 0.903 +/- 0.003 | 0.211 +/- 0.005 | 33.9 | ||
fastPhase | 0.924 +/- 0.001 | 0.134 +/- 0.004 | 147.5 | 0.907 +/- 0.002 | 0.241 +/- 0.006 | 134.6 | ||
PL-EM | 0.913 +/- 0.003 | 0.140 +/- 0.003 | 1.0 | 0.854 +/- 0.004 | 0.225 +/- 0.005 | 12.6 | ||
2snp | NA | 0.176 +/- 0.002 | < 0.1 | NA | 0.283 +/- 0.004 | < 0.1 | ||
2B. APOE dataset | ||||||||
Soft | MD | IF | IER | Time (sec.) | MD | IF | IER | Time (sec.) |
Ishape1 | 0% | 0.946 +/- 0.001 | 0.062 +/- 0.001 | 0.2 | 5% | 0.932 +/- 0.003 | 0.109 +/- 0.005 | 0.4 |
Ishape2 | 0.941 +/- 0.001 | 0.057 +/- 0.001 | 3.5 | 0.926 +/- 0.003 | 0.102 +/- 0.005 | 4.1 | ||
Phase2.1 | 0.940 +/- 0.001 | 0.055 +/- 0.001 | 14.0 | 0.923 +/- 0.003 | 0.102 +/- 0.005 | 15.8 | ||
Phase1.0 | 0.947 +/- 0.001 | 0.062 +/- 0.000 | 2.7 | 0.932 +/- 0.003 | 0.108 +/- 0.005 | 3.9 | ||
fastPhase | 0.876 +/- 0.001 | 0.118 +/- 0.002 | 49.1 | 0.870 +/- 0.003 | 0.181 +/- 0.005 | 44.2 | ||
PL-EM | 0.897 +/- 0.000 | 0.125 +/- 0.000 | 0.1 | 0.883 +/- 0.004 | 0.159 +/- 0.005 | 0.4 | ||
2snp | NA | 0.200 +/- 0.000 | < 0.1 | NA | 0.227 +/- 0.004 | < 0.1 | ||
Ishape1 | 2% | 0.942 +/- 0.002 | 0.078 +/- 0.003 | 0.3 | 10% | 0.917 +/- 0.004 | 0.149 +/- 0.007 | 0.6 |
Ishape2 | 0.935 +/- 0.002 | 0.070 +/- 0.003 | 3.9 | 0.910 +/- 0.004 | 0.143 +/- 0.007 | 4.6 | ||
Phase2.1 | 0.933 +/- 0.002 | 0.072 +/- 0.003 | 14.8 | 0.907 +/- 0.004 | 0.146 +/- 0.007 | 17.4 | ||
Phase1.0 | 0.941 +/- 0.002 | 0.078 +/- 0.003 | 3.2 | 0.917 +/- 0.004 | 0.150 +/- 0.007 | 5.1 | ||
fastPhase | 0.875 +/- 0.002 | 0.140 +/- 0.003 | 47.0 | 0.864 +/- 0.004 | 0.225 +/- 0.007 | 45.4 | ||
PL-EM | 0.894 +/- 0.003 | 0.137 +/- 0.003 | 0.2 | 0.854 +/- 0.005 | 0.191 +/- 0.006 | 1.3 | ||
2snp | NA | 0.208 +/- 0.002 | < 0.1 | NA | 0.259 +/- 0.004 | < 0.1 | ||