HLA haplotype analysis

[Nilaksha]

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.

[BurlEarl]

Could you be more specific on that hypotheses you would like to test. Are you just looking for enriched haplotypes in the study/control? i am in a MHC/HLA lab (sort of) and some of my coworkers might have a good idea for you.

Cheers

[akhattri]

What worked best for your data? let me know?

Thanks