Question: Gwas Stepwise Tutorial
7
gravatar for always_learning
6.2 years ago by
always_learning1000
Doha, Qatar
always_learning1000 wrote:

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 !!

vcf gwas ngs 1000genomes • 13k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by always_learning1000

See How To Get Started Learning Gwas Analysis

ADD REPLYlink written 6.2 years ago by zx87548.4k
5
gravatar for Istvan Albert
6.2 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

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

ADD COMMENTlink written 6.2 years ago by Istvan Albert ♦♦ 81k
4
gravatar for ugly.betty77
6.2 years ago by
ugly.betty771.0k
United States
ugly.betty771.0k wrote:

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 :)

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by ugly.betty771.0k
1
gravatar for always_learning
6.2 years ago by
always_learning1000
Doha, Qatar
always_learning1000 wrote:

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 ]

ADD COMMENTlink written 6.2 years ago by always_learning1000

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.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Istvan Albert ♦♦ 81k
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