I'm using PopGenome R package to calculate Fst with vcf files. I met some problems during the protocol
First, I want to analyze whole genome level data. In the manual of PopGenome, it says I should input a specific chromosome or scaffold name. If I want to generate Fst of whole genome, what should I input? The function of read data seems unavailable for me after I tried many times using the function .
Second, how can I set the "numcol" column if I have 1.7*10E7 SNP sites in my data?
I have about 7000 scaffolds in my reference genome, it seems I should write a R script to make PopGenome package calculate Fst ?