Question: GWAS analysis tool
4
gravatar for arshad1292
22 months ago by
arshad129240
arshad129240 wrote:

I am going to start GWAS analysis for human genome. Any recommendation which tools should I use? Also, it would be great if you could please send me a link to tutorial with mock data so I can practice first before working on the real data.

I am new to GWAS analysis so please help me. Many thanks in advance.

snp R genome • 2.3k views
ADD COMMENTlink modified 18 months ago by breckuh30 • written 22 months ago by arshad129240

Many thanks for your response. I have been busy and now starting to work on this. Cheers!

ADD REPLYlink written 20 months ago by arshad129240
3
gravatar for zx8754
22 months ago by
zx87549.2k
London
zx87549.2k wrote:

Read about plink and search for "plink tutorial GWAS". Also, related biostars post:

Analyzing Genomewide Association Study Data: A Tutorial Using Plink
Course: Practical GWAS Using Linux and R

There are many R packages, too:

https://www.ncbi.nlm.nih.gov/pubmed/28132152
https://bioconductor.org/packages/release/bioc/html/GWASTools.html
https://github.com/JoniColeman/gwas_scripts
https://poissonisfish.wordpress.com/2017/10/09/genome-wide-association-studies-in-r/

ADD COMMENTlink modified 22 months ago • written 22 months ago by zx87549.2k
2
gravatar for breckuh
18 months ago by
breckuh30
breckuh30 wrote:

I would recommend the book "Genome-Wide Association Studies and Genomic Predictions". It was published in 2013, so I thought it might be outdated given the newness and pace of the GWAS field, but I've found many of the chapters to be highly relevant, and they have saved me a lot of time with my first GWAS project, particularly the chapters related to quality control and plink.

ADD COMMENTlink written 18 months ago by breckuh30
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