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5.1 Introduction to genedrop.

genedrop simulates data, on a pedigree, for analysis by other programs. It simulates, for each individual in a pedigree, genotypes of linked or unlinked marker loci and the discrete genotypes and polygenic values contributing to quantitative traits. The trait loci may or may not be linked to marker maps.

An option is to include founder labels with the output pedigree. For each descendant, a pair of labels for each marker or trait identifies the founders who are the maternal and paternal ancestors for the genotype at this locus.

The order of simulation of markers and traits is: for each individual, the marker genes, if any, are first 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.

The user may provide 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) are specified by the user. Several different trait models can be specified as in the following table:

Means Zero additive variance Non-zero additive variance
equal non-genetic model polygenic model
unequal major gene model mixed-model

Note that the trait must be biallelic 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.

To leave some individuals in the simulated pedigree data as "missing", specify them as "unobserved" in the input pedigree file with the observed indicator.


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