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software for multiple phenotype-to-genotype associations

We have a suite of antibodies (~50) that recognize allele-specific antigens, and would like to associate each antibody with its corresponding variant(s). The gene product for each antibody is known, and we have WES and antibody reactivity information for ~1000 individuals. Is PLINK the most suitable tool for this analysis, or are there tools better suited for mapping multiple phenotype-genotype associations?

snp phenotype association
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written by harold.smith.tarheel harold.smith.tarheel

1 answer

I assume you are calling SNPs from your WES data.

PLINK is good and easy to use. However, my favorite is genabel! Also, I have some colleagues that are very happy with EMMAx, included in the epacts pipeline

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written by Fabio Marroni Fabio Marroni

Yes to SNP calling from WES - should have been explicit on that point. Thanks for the other tool suggestions.

EDIT: If you convert your post from comment to answer, I can accept it.

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written by harold.smith.tarheel harold.smith.tarheel

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