I merged two sets of SNP data. One set had all individuals (in that set) as 0 or -9 to indicate missing. The other set had all individuals set as 1 to indicate unaffected/control.

Now, I am trying to use convertf to change the data from ped to eigenstrat, but it keeps ignoring all the samples with missing phenotypes.

Does anyone know how would I recode the phenotypes in Plink (or how would I get convertf to not ignore any samples)?

Thanks!

-Deven