I have SNP data in VCF format as well as a gtf file with defined positions for genes. Does anyone know of a quick way (eg, using VCFtools) to calculate both the average Fst for a predefined set of coordinates as well as the per site Fst for that particular window? (specifically the max Fst value for that window). Doing either is rather easy but I'm looking for a way to save some time to get both statistics as the same output. Ultimately I want to get the max fst and avg fst for each gene in my data.

Thanks in advance!