Using publicly available dataset as control for GWAS
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7 months ago

I am aware of the limitations, and potential false positives that can arise in using a publicly available dataset as a control for a GWAS-like SNP association analysis. I was wondering if it would be possible to use a vcf like the one provided by gnomAD to use as a control.

I want to use the whole genome one (~460gb) one provided here https://gnomad.broadinstitute.org/downloads/, but I can only find allele frequencies, not genotypes per patient. Is there any way I could run an association test just with the allele frequency vcf? Thanks in advance

gwas gnomAD SNP variant vcf • 312 views
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