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?
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written
by
Lukáš •
1 answer
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)
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My appology for anybody whose reading this post. I know it is little out of topic, but i am really despread right now.