Error: Locus has more than 2 alleles

[roguestorm78]

Hi all,

I've come across this 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).  

Any ideas?

[Christopher Chang]

This error implies that individuals #1 and #2 have A and T genotypes at the locus.  Assuming that's correct, this is a triallelic SNP which cannot currently be handled by PLINK.

[roguestorm78]

Thank you Christopher - this is very helpful!

Jo