How vcftools calculate Fst value?

Question

[seta]

Hi all,

I used vcftools for calculation the Fst value between two populations (pop1 and pop2) using the below command:

./vcftools --vcf file.vcf --weir-fst-pop population_1.txt --weir-fst-pop population_2.txt  --out pop1_vs_pop2

However, some Fst value sounds strange to me. For example, please consider the allele frequency of some variants in two pops and the obtained Fst value:

SNP AF_pop1     AF_pop2     Fst value
snp1    0.74    0.43    0.037
snp2    0.33    0.79    0.423
snp3    0.69    0.03    0.42

As you see, the frequency of snp1 and snp2 is similar between the two populations, but there is a huge difference in the related Fst values. Similarly, while the allele frequency of snp2 and snp3 is very different between populations, the related Fst values are similar. I'm confused with such an output. Could you please let me know your idea about it, is it reasonable to you?

Thank in advance

[Kevin Blighe]

You may contact one of the developers of VCFtools (Adam Auton) in order to understand what is exactly happening. You should be able to find his contact online.