I'm trying to run Tajima's D over a certain region and for some regions it works fine but for others it gives me a blank output. For example I will run this code:

vcftools --vcf S_chilense.filt.vcf --from-bp 43721060 --to-bp 43721301 --chr Scaffold_8756_Chr6 --TajimaD 234 -c

and get this output:

CHROM   BIN_START   N_SNPS  TajimaD

There are variants in the VCF file between these positions, but the vcftools won't run an analysis past a certain bp region that ends around 43718000.

Does anyone have experience with this? This ends up missing a lot of variants at several different positions in my analysis.