04 Run GWAS - WheelerLab/gwasqc_pipeline GitHub Wiki

Running GWAS itself is a fairly trivial procedure. The action itself only requires as little as two lines of code, presuming the user already has a phenotype file readily available. Making a proper phenotype file is in itself trivial. As such, I will not discuss how to make a phenotype file, but I will describe the proper format of a phenotype file for user interest.

Phenotype file format

Run GWAS

Generate QQplots

For validation of a significant signal I have included a comprehensive script to plot partial or complete QQplots. As this script has more options than most of the other rscripts and is intended for frequent use I have written a more in depth wiki page.