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?
you could use `bcftools contrast`  https://samtools.github.io/bcftools/howtos/plugins.html

> runs a basic association test, per-site or in a region, and checks for novel alleles and genotypes in two 
>
> groups of samples. Adds the following INFO annotations:
> 
>  PASSOC .. Fisher’s exact test probability of genotypic association (REF vs non-REF allele)

