Hardy-Weinberg Option In Vcftools

Question

[Evanescent]

Hi all, I am trying to filter according to the Hardy-Weinberg Equilibrium test. I use the following:

vcftools --vcf myfile.vcf --hardy

and I got: Error:Require Genotypes in VCF file in order to output HWE Statistics.

despite the fact the values for GT:AD:DP:GQ:PL are present in the file. What am I missing ?

Thanks !

Answer 1

[Adam]

Sounds odd, but difficult to help without seeing the VCF file. The best way to get help would be to email the VCFtools help mailing list ([e-mail]) with a small sample (a few dozen lines, including header) of your VCF file.