Table 2 Thresholds of three different algorithms to infer haplotype block
From: Evaluation of sample size effect on the identification of haplotype blocks
Algorithms | Thresholds | |
|---|---|---|
1 | Four-gametes test (recombination-based) | Threshold of forth gamete's haplotype frequency: 0.01 |
2 | Gabriel's method (LD-based) | Confidence interval threshold for strong LD (lower side): 0.70 Confidence interval threshold for strong LD (upper side): 0.98 Upper confidence interval maximum for strong recombination: 0.90 Threshold of strong LD rate in region: 0.95 |
3 | Kamatani's method (diversity-based) | Threshold of |D'| for initial clustering: 0.90 Threshold of haplotype frequency adding neighboring SNPs: 0.01 |