Question: GWAS analysis tool
4
gravatar for arshad1292
10 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 • 1.3k views
ADD COMMENTlink modified 6 months ago by breckuh20 • written 10 months ago by arshad129240

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

ADD REPLYlink written 8 months ago by arshad129240
2
gravatar for zx8754
10 months ago by
zx87547.3k
London
zx87547.3k 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 10 months ago • written 10 months ago by zx87547.3k
1
gravatar for breckuh
6 months ago by
breckuh20
breckuh20 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 It was published in 2013, so I thought it might be outdated given the newness and pace of the GWAS field, but I've found many of the chapters to be highly relevant, and they have saved me a lot of time with my first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 6 months ago by breckuh20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 774 users visited in the last hour