The ped file

SeqSIMLA generates ped files in LINKAGE format. The first six columns are the same as the pedigree structure file. Then every two columns specify the two alleles for each marker. The alleles are coded as 1 or 2.

For example,

FAM1 1 0 0 1 1 1 1 2 2
FAM1 2 0 0 2 1 1 2 1 1
FAM1 3 1 2 1 2 1 2 1 2
FAM1 4 0 0 2 1 2 2 1 1
FAM1 5 3 4 1 2 1 2 1 2
FAM2 1 0 0 1 1 1 1 1 2
FAM2 2 0 0 2 1 2 2 1 2
FAM2 3 1 2 1 2 1 2 1 1

The ped file has two markers. The alleles for the first marker are specified in columns 7 and 8. The alleles for the second marker are specified in columns 9 and 10. The total number of columns in a ped file should be 6+2xM, where M is the number of markers. Note that allele 1 or 2 is not necessarily a minor or major allele. It depends on whether 1 or 2 appears to be the minor or major allele in the reference sequence file.