From: Software for tag single nucleotide polymorphism selection
Program | Block definition | Tag criteria | Tag SNPs in block 1, as defined by Haploview | Tag SNPs in block 2, as defined by Haploview | htSNPs not in blocks, as defined by Haploview |
---|---|---|---|---|---|
LDSelect | N/A | Pairwise R2 | 1, 2 | 5, 6, 7, 13 | 4, 15 |
Haploview | Gabriel defaulta | Not stated | 1, 2 | 5, 6, 7, 13 | N/A |
htSNP | Used results of Haploview |
| 1, 2 | 5, 7, 8, 13 | N/A |
TagIT | Used results of Haploview |
| 1, 2 | 5, 6, 13, 14 | N/A |
tagSNPs | Used results of Haploview |
| 1, 2 | 5, 6, 13 | N/A |
 |  |
| 1, 2 | 5, 7, 8, 13 | N/A |
Hapblock | Empirical LD optionb |
| 1, 2 | 5, 9, 13 | 4 |
 |  | I e | 1, 2 | 5, 7, 13 | 4 |
 |  | Pairwise R2 | 1, 2 | 5, 6, 7, 13 | 4, 15 |
Tagger | N/A | Pairwise R2 | 2, 3 | 5, 6, 10, 13 | 4, 15 |
 |  | Restricted | 2, 3 | 5, 10, 13 | 4, 15 |