1.global Fst

vcftools --vcf QC.vcf --weir-fst-pop A --weir-fst-pop B --weir-fst-pop C --weir-fst-pop D --weir-fst-pop E --weir-fst-pop F --fst-window-size 50000 --fst-window-step 25000 --out global_FST

筛选出来的Fst值较大的区域，意味着在这些群体间的分布不均匀，对于研究单个群体没什么用

2.群体Fst

The average FST and associated P values over all sliding windows were regarded as the values at the whole-genome level.

Pairwisegenome-wide FST values also indicated that genomic differentia-tion between landraces and improved breeds (FST = 0.032, P=0.041) was less than that between Asiatic mouflon and landraces (FST = 0.125, P= 0.015) or between Asiatic mouflon and
improved breeds (FST = 0.132, P= 0.016).

《Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits》

尽管这里的Fst值不是使用常规的vcftools计算，但道理是一样的