Hey there!

I have a VCF file with roughly 8 million SNPs and I would like to calculate the significance of Fst per SNP in order to identify loci under selection between my different populations.

The idea is to use the HierFstat package to calculate Fst and then use the function boot.ppfst to test the significance of FST values (CI). By the way, how would you define the quantiles for bootstrapped CI? Default is quant=c(0.025,0.975)

I´ve seen similar questions here but since I´m specifically reading a VCF file with read.VCF that gives a dosage format, not fstat format so I´m a bit lost here...

I´ve tried the fs.dosage function but gives the overall Fst on a population basis, something I don´t need.

I any of you could provide some help I would be very glad :)

All the best,

Jesús