Table 2. Parameter tuning of ANCHAP, SLRP and fastIBD.
| Method | Parameters and values | Sensitivity | False discovery rate |
|---|---|---|---|
| ANCHAP | IBD threshold Stage I: 3 cM | 0.81 | 0.010 |
| IBD threshold Stage III: 2 cM | |||
| Overlap threshold: 10 markers | |||
| Mismatch tolerance: 2% | |||
| Minimum phase information: 100 markers | |||
| SLRP | Default | 0.76 | 0.008 |
| ExpectedIBS: 1 cM | |||
| ExpectedIBD: 10 cM | |||
| SLRP | Empirical | 0.77 | 0.011 |
| ExpectedIBS: 0.42 cM | |||
| ExpectedIBD: 9.17 cM | |||
| fastIBD | Scale: 1 | 0.27 | 0.000 |
| fastIBD | Scale: 2.8 | 0.80 | 0.021 |
| fastIBD | Scale: 2.9 | 0.81 | 0.024 |
| fastIBD | Scale: 3 | 0.83 | 0.024 |
| fastIBD | Scale: 4 | 0.87 | 0.044 |
Abbreviations: IBD, identity by descent; SLRP, systematic long-range phasing; ORCADES, Orkney Complex Disease Study.
Experiments with data from chromosome 2, and 597 ORCADES individuals with their genotyped parents removed. The identified regions of IBD were evaluated against phased haplotypes of 58 individuals who could be phased using the genotypes of their parents. Highlighted rows indicate parameters used in genome-wide analysis.