Deciding on a hardy-weinberg filter for case-only dataset

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6.7 years ago

lalir ▴ 10

Hello,

I currently have a dataset consisting of approximately 500 disease cases with exome sequencing data. I understand hardy-weinberg filters are typically applied to controls, but was wondering if conducing quality control on a case population would alter the stringency of the filter.

I am currently using a filter of P < 0.05 to be conservative. The p-values are generated via a chi-squared test using vcftools --hardy.

Any insight on this matter would be greatly appreciated!

Thank you.

next-gen hardy-wienberg QC • 2.0k views

ADD COMMENT • link 6.7 years ago by lalir ▴ 10

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An actual association can cause deviations from HWE. I am not sure whether you would actually want to filter those SNPs. Why not just flag them for further analysis (for instance to check if the deviation was caused by genotyping errors, in case they were genome-wide significant? Have you checked this paper?:https://www.ncbi.nlm.nih.gov/pubmed/18428419

ADD REPLY • link 6.7 years ago by GabrielMontenegro ▴ 670

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