7.4 ibddrop statements

• Use the `simulate' statement to specify simulation of markers and one linked or unlinked trait, for each of one or more chromosomes (see genedrop computing requests).
• Use `map' statements to specify the marker and trait maps (see genedrop mapping model parameters).

Note that ibddrop does not simulate or use marker or trait data. The statements are used only to specify the map of the loci at at which descent is to be simulated and ibd scored. The locations of loci are specified in this way so that direct comparisons can be made between output of ibddrop and of lm_auto (see Running lm_auto example and sample output), where simulation is conditional on marker and trait data.

set [component M] proband gametes N1 K1 N2 K2...

In this statement, the user specifies which gametes ibddrop is to score. Each statement must contain gametes from a single component, as the components are assumed to be independent, i.e. the probability of ibd between gametes from different components is zero. Pairs consisting of an individual's name and a meiosis indicator are listed, with `0' indicating the individual's maternal gamete and `1' indicating their paternal gamete.

In the current version of MORGAN, the number of proband gametes in a set is limited to 10.

set [chromosome I] locus window K

This statement gives the window size (number of loci) for which the multilocus ibd probabilities are scored. If no size is given, each locus is scored separately.

set sampler seeds H1 H2

This statement initializes a pair of seeds for the random number generator. The seeds must be positive and no greater than `0xFFFFFFFF', with the first seed (congruential seed) odd, and the second seed (Tausworthe seed) nonzero. If no seeds are specified, default seeds are used.

set MC iterations I

Required. This statement specifies the total number of Monte Carlo iterations.

simulate markers K1 trait 1

This statement specifies the number of markers to be simulated, as well as a linked trait. A linked or unlinked trait must be specified.

simulate unlinked trait 1

This statement specifies a trait to be simulated that is not linked to markers. Only one trait can be simulated and this trait will be placed to the left of all markers.