More than 50%of SNPs are missing
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Hi, I am currently working on the HLA imputation of a Norwegian cohort, using SNPs. Every time I launch the HIBAG R script, whether I use the pre-fit models or build and predict in parallel, I always get the warning “More than 50% of SNPs are missing!”. I have checked the input PLINK files I use, and they contain most of SNPs IDs (252/275) coming from the HapMap_CEU_Geno$snp.id list. Could you tell me what can trigger this warning to appear in the R code you wrote, so I can correct my use of your software?
Thank you.
I guess it depends on your genotype platform. If you use immuno-chip then the model should be derived from immuno-chip, otherwise you would have a low mapping rate.
Please use platform-specific models