6.5.1 markerdrop computing requests

markerdrop requires one of the following two statements:

simulate markers J using trait

This statement requests the simulation of J markers conditional on a trait model. If marker data are simulated conditional on a trait model, the user must specify trait allele frequencies, genotypic penetrances and a map position for the trait locus within the parameter file. Affection status of each individual must be specified in the pedigree file following gender, if present.

simulate markers J using inheritance

This statement requests the simulation of J markers conditional on an inheritance pattern at the trait locus. If marker data are to be simulated conditional on an inheritance pattern, the user must specify a map position for the trait within the parameter file. In addition, a pair of inheritance indicators for each individual must be included in the pedigree file following gender, if present. The first of the pair describes paternal inheritance at the trait locus and the second describes maternal inheritance. Inheritance indicators are coded as `0', `1' or `-1', corresponding to segregation of the trait allele from the individual's grandmother, grandfather, or unknown, respectively. For example, `0 0' indicates that the individual inherited the alleles carried by both grandmothers at the trait locus, while `0 1' indicates inheritance of the paternal grandmother's and maternal grandfather's alleles.