What is the best tool to apply Hardy-Weinburg Equilibrium filtering to find variants in a pVCF with a p-value > a given threshold (10^-15)? Permanently deleted user 10 August 2022 00:00 1 comment I tried vcftools but could not get it to work. Comments 1 comment Sort by Date Votes Ondrej Klempir DNAnexus Team 14 September 2022 12:42 I would suggest working with pVCF using Hail: https://github.com/dnanexus/OpenBio/tree/master/hail_tutorialhttps://documentation.dnanexus.com/science/using-hail-to-analyze-genomic-data Alternatively, I would check PLINK documentation: https://www.cog-genomics.org/plink/1.9/filter 0 Please sign in to leave a comment.
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I would suggest working with pVCF using Hail: https://github.com/dnanexus/OpenBio/tree/master/hail_tutorial
https://documentation.dnanexus.com/science/using-hail-to-analyze-genomic-data
Alternatively, I would check PLINK documentation: https://www.cog-genomics.org/plink/1.9/filter
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