About the INFO value in Quality Control of GWAS summary statistics

privefl / bigsnpr

R package for the analysis of massive SNP arrays.

https://privefl.github.io/bigsnpr/

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About the INFO value in Quality Control of GWAS summary statistics #509

Open koujiaodahan opened 1 month ago

koujiaodahan commented 1 month ago

We run the gwas based on our WGS dataset ,so no imputation ,no INFO value. So is there no need to run the Quality Control of GWAS summary statistics?

privefl commented 1 month ago

Are you talking about the QC comparing the two estimates of SD? Yes, it is always good to check for potential errors. You can also compare AFs between your GWAS dataset and the LD reference.

privefl commented 1 month ago

Any update on this?