I make ped and map file on shell, when I read file by plink I get below problem;
./plink --file test --noweb --missing-genotype N
54241 (of 54241) markers to be included from [ test.map ]
ERROR: Locus 1 has >2 alleles: individual R921C12 273487 has genotype [ T C ] but we've already seen [ - ] and [ T ]
I cheak my file, I seems ok, the data is indeed 'CC' with no -'s or T's nearby! the length of each line (i.e. for each individual) is consistent throughout. I've tried both tab- and space-demilited files, but no difference. I dont undrestand why I get this error. this is the raw which I get that problem:
R921C12 273487 2950577 2950350 1 Resistant C C T T T T C C T T . . .