Question: software for multiple phenotype-to-genotype associations
0
gravatar for harold.smith.tarheel
21 months ago by
United States
harold.smith.tarheel4.3k wrote:

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 • 493 views
ADD COMMENTlink written 21 months ago by harold.smith.tarheel4.3k
2
gravatar for Fabio Marroni
21 months ago by
Fabio Marroni2.1k
Italy
Fabio Marroni2.1k wrote:

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

ADD COMMENTlink modified 21 months ago • written 21 months ago by Fabio Marroni2.1k

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.

ADD REPLYlink modified 21 months ago • written 21 months ago by harold.smith.tarheel4.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1450 users visited in the last hour