software for multiple phenotype-to-genotype associations

Question

[harold.smith.tarheel]

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?

Answer 1

[Fabio Marroni]

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

[harold.smith.tarheel]

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.