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HLAassoc #8

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DelnazRoshandel opened this issue Jun 30, 2021 · 2 comments
Open

HLAassoc #8

DelnazRoshandel opened this issue Jun 30, 2021 · 2 comments

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@DelnazRoshandel
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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
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catheriz commented Sep 2, 2021

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

@WansonChoi
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@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.

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@WansonChoi @catheriz @DelnazRoshandel