I've come across a problem in PLINK when trying to do a Fishers exact test. The command I'm using is as follows:
plink --file test --fisher --allow-no-sex --1
And the error I get is:
ERROR: Locus 1:54208 has >2 alleles
Individual Ind3 Ind3 has genotype [ G G ] but we've already seen [ A ] and [ T ]
I've checked my file rigorously and the data is indeed 'GG' with no A's or T's nearby! I also have no missing data. 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 haven't found any special characters etc. either (using vi :set list).
Interestingly, I've taken Ind3 out of the file and re-run the test, but the same error is thrown up (but now obviously on Ind4, which is now on line 3).