6.1 Introduction to markerdrop

markerdrop simulates marker data at markers linked to a potential trait locus. The user must specify whether marker data simulation is to be conditional on a trait model or on an inheritance pattern at the trait locus. The choice of a trait model or an inheritance pattern will dictate which additional parameter statements must (or may) be included in the parameter file.

• If marker data simulation is to be conditional on a trait model, parameters must be provided for trait locus allele frequencies using `set traits frequencies', for genotypic penetrances using `set incomplete penetrances', and for the map position of the trait locus using a `map' statement see markerdrop statements. There must be only one mapping statement for the trait; from this statement the trait number (name) is deduced. Phenotypic trait data are provided as affection status of each individual in the pedigree file. An inheritance pattern at the trait locus is simulated from the trait data; this becomes the trait model on which markers are simulated.

• If marker data simulation is to be conditional on an inheritance pattern at the trait locus, the partially specified segregation pattern at the trait locus is provided in the pedigree file using inheritance indicators. For more information on inheritance indicators, see markerdrop computing requests and Using MCMC to Estimate Parameters of Interest in Pedigree Data. Location of inheritance indicators in the pedigree file can be specified using the `input pedigree record' statement. Again, specification of a map position for the trait locus using a `map' statement is required.