6.5.2 markerdrop mapping model parameters

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

This statement is required for markerdrop if more than one marker is to be simulated. It specifies the marker map (optionally a sex-specific map), in units of genetic distance (cM), marker position (cM), or recombination fraction. If distance is selected, markerdrop will expect one fewer values than the number of markers, as these are intermarker distances. If position is expected, the same number of values as markers will be expected, as these are the positions of the markers relative to some zero point to the left of marker 1. If Kosambi is not specified, the Haldane mapping function is used to convert between genetic distance and recombination fraction.

map [gender (F | M)] trait K marker J ( [Kosambi] distance | recombination fraction ) X

This statement is required for markerdrop; it tells the program which trait to use in the simulation of marker data and gives a location for the trait locus, either as a map distance or recombination fraction, following the marker listed in the statement. As with genedrop, to simulate a trait locus position that precedes all markers, list the marker number as `0'.