How to force missing values for genotype?

Question

[aritra90]

Hi,

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.

Answer 1

[chrchang523]

See the Plink manual : Set blocks of genotype calls to missing

Set blocks of genotype calls to missing
--zero-cluster <filename>

If clusters have been defined, --zero-cluster takes a file with variant IDs in the first column and cluster IDs in the second, and sets all the corresponding genotype calls to missing. See the PLINK 1.07 documentation for an example.

This flag must now be used with --make-bed and no other output commands (since PLINK no longer keeps the entire genotype matrix in memory).