Search this site for GWAS tutorials and see posts like this:

• Good GWAS papers / resources
• Need recommendation on good tutorials for performing GWAS

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.

http://www.barnesandnoble.com/listing/2689438569150?r=1&cm_mmca2=pla&cm_mmc=GooglePLA-_-TextBook_NotInStock_26To75-_-Q000000633-_-2689438569150

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.

http://ecodevoevo.blogspot.com/2013/08/cystic-fibrosis-genetic-variation-and.html

We covered his blog and issues related to GWAS here:

http://www.homolog.us/blogs/blog/2013/07/30/battle-over-gwas-ken-weiss-edition/

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"

http://thefinchandpea.com/2013/08/23/we-still-dont-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 :)

Hi All, Thanks all !! I made a very good progress on this !! Thanks every one !! But I have some very basic doubt still :

1) How do we get files .bed and .map format ? [ I guess that we will convert vcf files to .bed format then what about .map format ]

2) How to do check if data has passed all standard checks? [ Any tool for this ]