Question: HLA typing analysis with plink or any other method?
0
gravatar for nilakshafreezon
4.7 years ago by
Sri Lanka
nilakshafreezon110 wrote:

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.

 

plink hla • 2.1k views
ADD COMMENTlink modified 4.7 years ago by Katie D'Aco1000 • written 4.7 years ago by nilakshafreezon110
1

Have you had a look at SNP2HLA?

ADD REPLYlink written 4.7 years ago by krobasky10

Seems interesting. I will take a closer look. But not sure whether It can be used in the analysis except for missing allele imputation. Thanks :)

 

ADD REPLYlink written 4.7 years ago by nilakshafreezon110
1
gravatar for Katie D'Aco
4.7 years ago by
Katie D'Aco1000
Massachusetts
Katie D'Aco1000 wrote:

Standard genetic association tools aren't well suited for HLA. I would use R to do a statistical test to check if any allele was present in an excess of cases or controls (I would do this at varying levels of resolution). You would have to do some research on the appropriate tests to use. AFIAK there are no existing tools for HLA association tests.

ADD COMMENTlink written 4.7 years ago by Katie D'Aco1000

Thanks for the information :)

ADD REPLYlink written 4.7 years ago by nilakshafreezon110
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