Hi, I have a set of HLA variants from a case control study annotated in tabulated files. I thought of analyzing them with plink and after a hard work, I tried to convert my raw data to plink supporting file formats. (.lgen,.map and .fam). Thought everything went smooth, but when I tried to run my data with plink I get,
ERROR: Locus rs1050517 has >2 alleles: individual 1060 106 has genotype [ G C ] but we've already seen [ G ] and [ A ]
Since HLA variants contains multiple alleles, this phenomena is possible but I didn't know plink only accepts SNPs if and only if they have two alleles. Am I missing something here? Or could you specify me a better tool to do some HLA variant analysis.
Thanks a lot in advance.