Hello everyone, I ran PCA to check for population stratification before imputation. Looking at the plot it seems i have a mixed population (EUR+AMR). I plan to impute using Michigan imputation server for which i need to choose the population of my uploaded data. My confusions:
1) Do i choose a mixed population as my sample population based on my PCA plots. (This dataset was presumably recruited from an European cohort but the PCA doesn't show a clearcut EUR population but a mixture of EUR+AMR).
2) What are the possible consequences if i choose to impute as a EUR population (i don't like this idea)
Thank you all.