Gwas Stepwise Tutorial

Question

[always_learning]

Hi All,

If we have some step by step tutorials for GWAS analysis ? Like I have VCF files and how to start from here ? I know its very basic question but I didn't work on GWAS till now either !!

[zx8754]

See How To Get Started Learning Gwas Analysis

Answer 1

[Istvan Albert]

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

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

Answer 2

[ugly.betty77]

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 :)

Answer 3

[always_learning]

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 ]

[Istvan Albert]

This is not a forum but a Q&A site. So do not add a new question as an answer to your original question. If you have new questions post them separately. Your last post will be deleted soon.