Table 3 Comparison of the performance of the genotype-calling methods with human data
MethodCorrect-Call Rate among Individuals (mean ± 2 SEM)Correct-Call Rate among Called Genotypes (mean ± 2 SEM)
BGC0.954 ± 0.00040.969 ± 0.0004
GATK0.923 ± 0.00040.943 ± 0.0004
Samtools0.966 ± 0.00040.966 ± 0.0004
ANGSD0.967 ± 0.00040.967 ± 0.0004
GATK + Beagle0.941 ± 0.00040.941 ± 0.0004
  • The correct-call rate among individuals is calculated among individuals with HapMap genotypes, where missing genotype calls are considered incorrect. On the other hand, the correct-call rate among called genotypes is calculated only among individuals with both HapMap genotypes and called genotypes, respectively.