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