Hello
I'm using plink/1.9b5. I am filtering my dataset with --geno 0.2, but I would like to filter both cases and controls separately and keep all variants in the same output file.
I've tried the --filter-cases/--filter-controls, but as the definition of this filter says, it causes only cases/controls to be included in the current analysis. Is there a way to filter cases and controls separately while having just one output?
Thank you in advance
1 answer
plink --bfile ... --geno 0.2 --filter-cases --write-snplist --out case_geno_filtered
plink --bfile ... --extract case_geno_filtered.snplist --geno 0.2 --filter-controls --write-snplist --out final
plink --bfile ... --extract final.snplist --make-bed
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