vcftools can calculate statistics such as pi and Fst using sliding windows.
I've noticed that windows in which the alternative allele is fixed are not taken into account. However, those appear in the VCF file.
N_VARIANTS for pi at window_x is 20, but the region in the vcf file reports 25 SNPs, 5 of which are hom-alt in all samples.
I would like to find a way to calculate the SNP density as it comes in the vcf file using the same boundaries reported by vcftools.
Is there a way to make vcftools to do this?