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immunogenomics / HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies
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HLAassoc #8

Open DelnazRoshandel opened 3 years ago

DelnazRoshandel commented 3 years ago

I used Michigan server for HLA imputation and now I want to used HLAassoc for association tests. I am wondering what HLAassoc uses for logistic/linear regression: dosage/genotype probabilities or genotypes (hard calls)?

catheriz commented 3 years ago

I have the same question. Does the package use plink for logistic regression analysis?

WansonChoi commented 3 years ago

@DelnazRoshandel @catheriz HLAassoc uses PLINK logistic/linear regression.

@DelnazRoshandel I'm sorry for the late checking. HLAassoc takes imputed VCF as input, so the former, dosage/genotype probabilities, is right.