Interpretting VCFtools popgen outputs

Question

[Riley]

I have used VCFtools to produce population genetic statistics on whole genome sequence data using the following command as an example:

vcftools --gzvcf my_file.vcf.gz --hardy --out my_stats.hwe

I have produced for outputs for my populations: allele frequency, Hardy-Weinberg equilibrium, heterozygosity, and nucleotide diversity (they end in .frq, .hwe, .het, and .windowed.pi, respectively)

Heterozygosity is a per-individual measure and the other a per-SNP.

I was wondering if anyone knows how to interpret the outputs and to turn them into stats that make sense and can be presented?

Thanks