GWAS - QC & Tutorials.

Question

[flight505]

Hi, 👋

I was looking through Biostars to find some good resources to get started. Unfortunately, most of the posts are really old 4+ years and many links are dead.

I was hoping to make a small collection of good explanatory reads for learning more about the QC part of GWAS. If someone has some tips, tricks, protocols, notebooks or other useful resources please share by posting.

Thanks

I can add this which I liked: A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis https://doi.org/10.1002/mpr.1608 It has a git with all the files to follow and replicate the files and process..

[Asaf]

What is your starting point? Do you have the genotypes or you should establish that first?

[flight505]

Thanks for replying. Right now I just have raw genotype data. I am starting from scratch.

[Asaf]

Although QTL rather than GWAS but QC should be the same: https://kbroman.org/qtl2/assets/vignettes/do_diagnostics.html In addition to avoid bad markers we now interpolate evenly dispersed positions in the genome instead of using the actual markers.

[flight505]

Thanks for the advice - I will definitely look into that

[zx8754]

most of the posts...

Please add the links to your post.

Answer 1

[Kevin Blighe]

My own selection / collection:

Quality Control

• Quality control procedures for genome-wide association studies
• Data quality control in genetic case-control association studies (credit: alessandrotestori7)

General GWAS / genetic studies

• A comprehensive review of genetic association studies
• Problems of reporting genetic associations with complex outcomes
• Common vs. rare allele hypotheses for complex diseases
• Rare and common variants: twenty arguments

Kevin

[flight505]

Thanks for sharing 👍

Answer 2

[alessandrotestori7]

One good protocol for QC is: PMID: 21085122

• Data quality control in genetic case-control association studies.