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Disease/Trait SNPs Enrichment Analysis

Hello Biostar Community!

I have got some GWAS SNPs in my sequencing data (exome).Can i do some enrichment analysis against the GWAS database to check whether these SNPs are significantly enriched in my data or not? If yes, then how to do it? Please guide.

snp sequencing
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updated by GouthamAtla GouthamAtla • written by tahseen.abbas • tahseen.abbas

Please tell us the format of the data that you have (VCF?; PLINK PED format?; something else?). Also, 'significantly enriched' for what? - gene ontology?; KEGG pathways?; ...?

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written by Kevin Blighe Kevin Blighe

1 answer

Hi, for this purpose, you need to use Coloc which tells if your SNPs are enriched within the genomic locations of any GWAS SNPs of particular trait.

I guess your statement I have got some GWAS SNPs in my sequencing data is not correct, because from exome-seq, you might have got SNPs and you wanted to check if they are strongly related to trait of your interests.

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written by GouthamAtla GouthamAtla

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