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HWE filter of vcf files

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

snp vcf.
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written by Max • Max

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

• 0 views • link
written by LauferVA LauferVA

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

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written by Max • Max

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