I was wondering how to force missing values in genotypes in PLINK format files?
I tried doing
--update-alleles followed by
--recode but that didn't work. I want to force some arbitrarily chosen marker's genotype values for some individuals to 0 (missing). In other words, I want to mask them for imputation (such that, doing
--missing will increase the missingness rate for the chosen marker)
I am not sure how to achieve this using PLINK. It'd be great if anyone has any idea on how to go about doing this.