Rare Variant Association analyses

Dear all,

I have a group of patients with a certain phenotype and healthy controls, and I need to do rare variant association analysis. The subjects already had g.vcf files and I obtained merged vcf file from them. Now, I need to do kinship and population stratification analysis in order to get unrelated European subjects. To this end, I would be very glad if you could recommend me any source (example/manual/review etc), which will be helpful for these steps and cont.?

Thank you very much in advance.

All the best