Table 1. Switch error rates for samples containing nominally unrelated individuals.
| Cohort | CARL | FVG | GPC | KOR | ORC | SPL | VB | VIS |
| Chip | 370K | 370K | 2.5S | 370K | 300K | 370K | 370K | 300K |
| N validation individuals | 130 | 274 | 419 | 118 | 201 | 50 | 481 | 150 |
| SLRP Yield | 71.82 | 73.82 | 45.17 | 67.52 | 88.15 | 31.82 | 87.63 | 71.09 |
| SHAPEIT2 (IBD) | 0.75 | 0.21 | 0.16 | 0.18 | 0.14 | 0.60 | 0.17 | 0.19 |
| SLRP (IBD) | 1.15 | 0.40 | 0.28 | 0.45 | 0.33 | 1.99 | 0.33 | 0.43 |
| Beagle (IBD) | 2.57 | 1.18 | 0.30 | 1.25 | 0.94 | 4.38 | 1.07 | 1.30 |
| HAPI-UR 3× (IBD) | 5.43 | 2.25 | 0.35 | 2.55 | 2.59 | 8.30 | 1.93 | 2.94 |
| SHAPEIT2 (No IBD) | 5.03 | 4.10 | 0.51 | 3.11 | 2.43 | 3.35 | 2.74 | 3.65 |
| Beagle (No IBD) | 7.73 | 5.72 | 0.84 | 5.55 | 5.05 | 6.00 | 5.03 | 6.36 |
| HAPI-UR 3× (No IBD) | 15.97 | 10.31 | 0.82 | 10.20 | 9.94 | 12.09 | 7.92 | 12.47 |
| SHAPEIT2 | 2.85 | 1.81 | 0.28 | 1.05 | 0.49 | 2.65 | 0.62 | 1.16 |
| Beagle | 5.31 | 3.11 | 0.49 | 2.53 | 1.78 | 5.57 | 1.88 | 2.78 |
| HAPI-UR 3× | 11.21 | 5.83 | 0.50 | 4.82 | 4.20 | 11.10 | 3.21 | 5.77 |
All individuals not explicitly related in the defined pedigrees were phased. We calculate overall SE rate (All), for chromosome 10 (this is not possible for SLRP) as well as SE rates within (IBD) and outside (no IBD) SLRP detected IBD regions. SHAPEIT2 consistently produces the most accurate haplotypes. Chip abbreviations: 370K - Illumina HumanHap 370CNV. 300K - Illumina HumanHap 300, 2.5S - Illumina Omni 2.5S.