From: Robust SNP genotyping by multiplex PCR and arrayed primer extension
Method | Call rate | Concordance with HapMap |
---|---|---|
Manual calling only | 100% | 99.92%1 |
MACGT (no cut-off) | 100% | 99.84%2 |
LDA (0 threshold) Total cases | 100% (1,941 cases vs. 1,941) | 99.89%3 (1,939 vs. 1,941) |
LDA (0 threshold) Homozygous cases | 100% (1,289 vs. 1,289) | 100%4 (1,289 vs. 1,289) |
LDA (0 threshold) Heterozygous cases | 100% (652 vs. 652) | 99.7%5 (650 vs. 652) |
MACGT (0.001 cut-off) | 94.04% | 99.94%6 |
LDA (0.65 threshold) Total cases | 99.18% (1,925 vs. 1,941) | 99.90%3 (1,923 vs. 1,925) |
LDA (0.65 threshold) Homozygous cases | 98.91%7 (1,275 vs. 1,289) | 100% (1,275 vs. 1,275) |
LDA (0.65 threshold) Heterozygous cases | 99.7% (650 vs. 652) | 99.7% (648 vs. 650) |