Applying Machine Learning on vcf file

I am learning machine learning for genomics data. I have a vcf file and I want to split my data into X and Y labels. I just want to know how can I do that ?? should I mark GT columns as 0/0 , 0/1, 1/1 into 1,2,3 and mark them as and rs ids as my predictors ??
I want to apply logistic regression on this.!