Following links are in addition to what Istvan recommended. They do not have step by step guide, but rather explain the scientific aspect of what GWAS researchers do.
As a starter, please check this book by professor Ken Weiss.
He also writes a very informative blog at http://ecodevoevo.blogspot.com/. Not all comments are directly related to GWAS, but you can check his today's writing on cystic fibrosis for example.
We covered his blog and issues related to GWAS here:
Also, Finch and the Pea blog posts informative commentaries on GWAS-related scientific issues. Please check
"We still don’t know why children resemble their parents"
Remember, science advances through consensus. Biggest advances like Darwin's theory and Mendel's discoveries were immediately accepted by the najority, and were widely 'retweeted' as soon as they appeared :)