SNP.loc << Marker Description File
SNP.ped << Pedigree genotypes 
SNP.out << File where results will be stored
0.005454  0.105365  0.889181 << IBD sharing probabilities at trait locus (z_0,z_1,z_2)
0 << Map function (0 Haldane, 1 Koshambi)
1 3 .5 0 << Points, Steps, Increment, offend
3 100 << CSI version (0 for original CSI), MC replicates 
.05 << alpha
.15 << percent missing markers allowed
