how to deal with missing genotype data (gt) to do a machine learning

Question

[arwa.ahmad95]

hi

I have a missing genotype data ./. and I want to encode genotype data to do machine learning algorithems

So I have 0/0 , 1/1 , 0/1 and ./. how can i encoded to do ML algorithems

thanks.

[Pierre Lindenbaum]

What is the scientific question you're trying to answer ?

[German.M.Demidov]

you can 1) naturally encode them as NA , NA is a special value to encode missing information "Non Available", 2) impute the missing genotypes prior to any downstream analysis.

[arwa.ahmad95]

how can I impute the missing genotypes? Is there any methods for imputing? Can u help me

[German.M.Demidov]

yes, there are multiple posts on biostars, starting from this I guess

Genotype Imputation