5.1 Introduction to genedrop.

genedrop simulates pedigree data for analysis by other programs. Given a genetic map, it simulates genotypes at marker loci (linked or unlinked) and the discrete genotypes and polygenic values contributing to quantitative traits. The trait loci may or may not be linked to marker maps. Thus, one or more of three kinds of loci are simulated on a chromosome: markers, traits linked to markers, and traits not linked to markers.

Using a random number generator, genedrop first assigns marker and trait genotypes and polygenic trait values to the founders. Then meiosis indicators are simulated for non-founders in chronological order, thus determining the genes inherited and the founder labels. The order of simulation of markers and traits for each individual is: first, the marker genes, if any, are simulated, in the order mapped on the chromosome. Then linked traits, if any, are simulated in map order. Finally, unlinked traits, if any, are simulated.

Because founders of a pedigree are assumed to be unrelated, a unique identifier, a founder gene label or founder label, is assigned to each of the two haploid genomes of each founder. The user may choose to include these founder labels with the output pedigree, identifying the ancestral source of each gene at each locus in non-founders.

The user may provide random number seeds for both the marker simulation and the trait simulation. This permits multiple simulations, for a pedigree, of identical marker genotypes, but with different quantitative trait values.

The population and segregation model parameters (allele frequencies, trait genotype means, additive and residual variances) may be specified by the user and take default values if not specified. Several different trait models can be specified as in the following table:

	Equal Genotypic Means	Zero Additive Variance
non-genetic model	YES	YES
polygenic model	YES	NO
major gene model	NO	YES
mixed model	NO	NO

The trait locus must be diallelic and the trait residual variance must be greater than zero. A very small residual variance can be specified if one desires to simulate a qualitative trait.

Genetic data on all individuals may be included in the simulated pedigree, or some individuals may be specified as "missing". If any individuals are to be missing genetic data, an "observed" indicator column must be included in the pedigree file. See Pedigree file, for details.