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  • Gene-level association test based on SNP data

    Hi,

    I've performed SNP calling from exome seq data followed by association testing (case-control), so I now have a p-value for each identified SNP.

    I would like to some how summarise the p-values for SNPs identified in the same gene, so that I get a p-value for each gene (for use in downstream analysis).

    So far I have been using the lowest p-value for each gene, but I wonder if this is really the best method..?

    So, what is the preferred method for this? And are there any tools for doing this?

    I hope someone can be helpful with this

    Best regards,
    Sara

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