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MAF in QC-ed summary stats #327

@gaow

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@gaow

In our gwas sumstats effect_allele_frequency / maf column are not qced, and is not recommended for use in the ananlysis according to @SamuelSun2000 . In our project, some of the dataset such as Kunkle_Stage1_2019 study do not have this column available, and this will make MR analysis unable to perform for this gwas cohort.

Two things we shold improve for RSS QC code:

  1. we should consider QC the effect allele frequency when there is a flip corrected, by adjusting the effect allele ferquencey accordingly
  2. For the GWAS data without MAF we can provide annotated MAF from our reference data.

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