HWE filter of vcf files

Question

[Max]

Hi

What is the appropriate approach to filter the snps(vcf format) with HWE parameter, Arlequin or vcftools. I've used vcftools for the advanced filer, like missing rate, MAF, etc. So i am wondering can i keep using it for the HWE. But i didn't see literatures using it instead they use Arlequin. So is it reliable using vcftools for HWE?

Thanks in advance

[LauferVA]

lets start with: what are the purposes of filtering based on HWE in the first place? why are you doing it (specifically)?

[Max]

filter the snps for the downstream analysis of population structure and genetics.