Penetrance for each genotype can be directly specified using a penetrance file. The file has two columns. The first column is the genotype and the second column is the penetrance for the genotype.For example,
The first column has genotypes for two disease loci. The genotypes for the two disease loci are coded by the minor allele counts. Therefore, 00 means locus 1 has genotype AA and locus 2 has genotype BB, where A and B are the major alleles. The probability of disease given genotype 00 is 0.05. 01 means locus 1 has genotype AA and locus 2 has genotype Bb. The probability of disease given genotype 01 is 0.06. The penetrance file provides a convenient way to specify the interaction effects. The order of the genotypes should correspond to the disease loci specified using -site. See the -site option for more details.