Calculating folded SFS to account for highly polymorphic regions

[space-beaver]

When plotting SNP density I generally have uniform distribution across the genome apart from on two chromosomes which each have small areas of high density. I've calculated the folded SFS per population and plotted it, and it shows a high excess of minor alleles in some populations. I'm concerned that this is driven by these highly polymorphic regions and wondered whether I can recalculate SAFs and SFS to account for this - either by subsampling these areas somehow, or excluding them entirely. Are there any options for this is ANGSD?

TIA