Hardy-Weinberg Option In Vcftools

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 !

vcftools snp vcf snp

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updated 14.4 years ago by Adam

• written 14.4 years ago by Evanescent •

1 answer

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 (vcftools-help@lists.sourceforge.net) with a small sample (a few dozen lines, including header) of your VCF file.

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written 14.4 years ago by Adam

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