I have vcf data from 95 people - 63 Cases and 32 controls. I filtered out possible pathogenic variations and now i want to know if variation in Cases samples apper significantly more often then in controls parth of sample.
I decided for Fst statistics done with vcftools. However I am not still 100% what am i doing.
Is there betters test to test for differenciations of two population? Is there any better tools then vcftools?