5.4.2 genedrop mapping model parameters

map [chromosome I] [gender (F | M)] marker ( [Kosambi] distances | recombination fractions | [Kosambi] positions) X1 X2...

This statement is required if simulation of more than one marker is requested. One statement is used per chromosome. This statement specifies the marker map or positions given in units of genetic distances (cM), or recombination fractions between markers. Marker map or positions can be sex-specific if gender is included in the statement. If `distances' is chosen, intermarker distances must be provided such that the number of distances is one less than the number of markers. If `positions' is chosen, the number of positions must equal the number of markers, as these are absolute positions relative to a zero point to the left of all of the markers. The Haldane mapping function is used to convert between the genetic distances and recombination fractions unless Kosambi is specified.

map [chromosome I] [gender (F | M)] traits K1 K2 ... markers J1 J2 ... ( [Kosambi] distances | recombination fractions) X1 X2...

This statement is required if simulated traits are to be linked to markers. That is, it is not required if no traits or only unlinked traits are to be simulated. The statement specifies the location of each trait locus with respect to one of the marker loci. Thus, the number of traits listed in the statement must be equal to the number of markers listed and to the number of distances (or recombination fractions) listed. The trait locus will follow the corresponding marker locus (to the right, so to speak) at the distance specified. To simulate a trait locus that precedes all marker loci, list marker `0' in the statement. For example, with `map trait 3 2 marker 6 0 distances 5 4', traits 3 and 2 will be placed 5 cM to the right of marker 6 and 4 cM to the left of marker 1, respectively.