2nd is your disease allele frequency. 3rd is number of penetrans classes. 4rd-6th lines is your penetrances. 7th line is you maximum number of alleles at any markers. 0.09 0.03 Name of the chromosome and then reconbination fractions separated by spaces between markers in pedrigree file.
Markers have to be in correct order in pedigree file.
If you get error messages, check out autoscan.out for more information. If in your material has been some mendelian errors, all information will be found from menderr.out file. After autoscan test has been run succesfully, you can start final scan. Autoscan has some limits and default values which you should know before you run autoscan. Maximum number of markers is 50 in one chromosome.