5.4.3 genedrop population model parameters

set [chromosome I] markers K1... frequencies X1 X2...

This statement specifies markers allele frequencies. Allele frequencies for a marker should sum to between 0.9999 and 1.0001. Otherwise they are normalized. Multiple markers can be specified in a single statement if they reside on the same chromosome and have the same number of alleles with the same allele frequencies.

set traits K1... frequencies X1 X2

This statement specifies the trait allele frequencies. Allele frequencies for a trait should sum to between 0.9999 and 1.0001. Otherwise they are normalized. Multiple trait loci can be specified in a single statement if they have the same allele frequencies. Trait loci must be biallelic.

set normalized frequencies

If the set of allele frequencies for each marker and trait is to be normalized, this statement is given. Normalization of the frequencies is recommended when simulating pedigree data, but not recommended when using the other programs.

set traits K1 ... genotype means X1 X2 X3

Since two alleles are simulated for each trait locus, three means must be specified for the polygenic trait values: one each for the (1 1), the (1 2) or (2 1), and the (2 2) genotypes. The default values 0.0, 0.0, and 0.0.

set traits K1 ... additive variance X

Here we specify the genetic variance for one or more trait. One of there statements is given for each value assigned. The default variance is 0.0.

set traits K1 ... residual variance X

This statement is like the preceding one. The environmental contribution to the trait is set using this statement.