what is the best way to combine several samples based on allele

Question

[Learner]

I have several exome data which I want to find differences across them. I did the analysis and annotation. Now I want to know which way would be best to combine them so that I know what is the differences between them based on allele

[Kevin Blighe]

It will depend on the formar of your data, which you have not stated. Typical programs include PLINK, but also SnpSift CaseControl.