Hi

I have converted files gen/sample (using gtool) to ped/map to be used in PLINK with phenotype coded as (0=unaffected 1=affected).

However, when I converted ped/map to bed/bim/fam the phenotype coding changed as well. (1=unaffected 2=affected).

Do you have any idea on how retain the initial phenotype coding as 0 and 1.