GWAS analysis tool

Question

[arshad1292]

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.

Answer 1

[zx8754]

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/

Answer 2

[breckuh]

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 It was published in 2013, so I thought it might be outdated given the newness and pace of the GWAS field, but I've found many of the chapters to be highly relevant, and they have saved me a lot of time with my first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.