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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