6.5.4 markerdrop computational parameters

set incomplete penetrances

This statement is required for markerdrop when using a trait model or when using inheritance indicators with a discrete trait. A penetrance, the probability of expressing the trait given a particular trait locus genotype, must be specified for each of the 3 possible genotypes at the trait locus. For example `set incomplete penetrances 0.15 0.85 0.99' specifies that the probability of expressing the trait is 0.15, 0.85 and 0.99 for (1,1), (1,2) and (2,2) trait locus genotypes, respectively.

set trait data discrete

This statement is optional. A discrete trait is the default when simulating using a trait model.

As with genedrop, marker seeds and trait seeds can be specified or the default values can be used, See genedrop computational parameters.