% Rcross -A -V -c SF2 -n 1000
Does a selfed F2 cross with 1000 offspring using the linkage map in qtlcart.map and the model in qtlcart.qtl. The command line options -A and -V turn off the interactive menu and the verbosity mode, respectively.
% Rcross -i cross.raw
Reads from the file cross.raw, tries to determine its format, and translates it if possible. The file cross.raw could be a MAPMAKER/QTL formatted file, a cross.inp formatted file or one that is already in the Rcross.out format.