I'm running vcftools on a vcf (obv, ha) to calculate Taijma's D in sliding windows of 10,000 bp:
vcftools --vcf in.vcf --out tajimasd --TajimaD 10000
The log file states that after filtering, kept 342087 out of a possible 342087 Sites (so all sites). Yet when I look at the output file, there are a lot of 'nan' (meaning no SNPs in that bin), and the bins that have Tajima's D calculated have a tiny number of SNPs in them (max 8 - certainly not adding up to >300k SNPs).
Any ideas as to why I'm getting no SNPs in the majority of my bins?