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SNP-set enrichment in GWAS analysis

I'm trying to see if a set of SNPs (prior candidates) are enriched in my GWAS results. This seems like something that should be do-able in PLINK, but I can't find an option... Does anyone know of a tool to do this?

Thanks.

snp enrichment gwas
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updated by Ram Ram • written by coleman_jonathan coleman_jonathan

1 answer

PLINK 1.07's --set-test flag may do what you need: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#set

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written by chrchang523 chrchang523

Thanks, Chris - don't know why I didn't spot that before!

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written by coleman_jonathan coleman_jonathan

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