Case-Control studies : How much Case-Cntrls samples differ from each other

Question

[Lukáš]

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?

[Lukáš]

My appology for anybody whose reading this post. I know it is little out of topic, but i am really despread right now.

Answer 1

[Pierre Lindenbaum]

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)