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  • HLA haplotype analysis

    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.

  • #2
    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
    --Please take everything thing I say with a grain of salt, because, if grad school has taught me anything, it's that I'm an idiot--

    Comment


    • #3
      What worked best for your data? let me know?

      Thanks

      Comment

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