Table 2 Genotype discordance rate of all SNPs, heterozygous SNPs and SNPs with maf <5 % in the real data analysis of Minnesota Center for Twin and Family Research
From: A computational method for genotype calling in family-based sequencing data
|  | All SNPs | Heterozygotes | SNPs with maf <5 % |
|---|---|---|---|
FamLDCaller (100 states) | 0.00080 | 0.0016 | 0.0035 |
FamLDCaller (200 states) | 0.00066 | 0.0012 | 0.0025 |
FamLDCaller (400 states) | 0.00056 | 0.0010 | 0.0018 |
FamLDCaller (600 states) | 0.00059 | 0.0010 | 0.0018 |
Beagle | 0.00105 | 0.0019 | 0.0027 |
Thunder (200 states) | 0.00116 | 0.0023 | 0.0042 |