Hi,

I calculated pairwise Fst using VCFTools:

```
vcftools --vcf input_data.vcf --weir-fst-pop population_1.txt --weir-fst-pop population_2.txt --out pop1_vs_pop2
```

What method I should use for statistical significance to determine the outlier region or loci under putative selection or differentiation.

Thanks in advance for help.

To follow up on Zev's suggestion 2, and if you still want to use vcftools, you can perform a permutation by permuting the individuals defined in the

`population_1.txt`

and`population_2.txt`

files.May you explain bit more how that can be done