Day 1 genetic association
Welcome to hands-on for the rare+SAIGE session of the 2023 International Statistical Genetics Workshop!
- Wei Zhou and Luke M. Evans
There are 4 tutorials corresponding to the 4 lectures, each introducing one method for genetic association tests.
| Practical | Method | Single-variant association tests (common variants) |
Set-based association tests (rare variants) |
Related samples | Case-control imbalance of binary traits |
|---|---|---|---|---|---|
| Part 1 | SPAtest | 😀 | 😀 | ||
| Part 2 | SAIGE | 😀 | 😀 | 😀 | |
| Part 3 | SKAT binary | 😀 | 😀 | ||
| Part 4 | SAIGE-GENE | 😀 | 😀 | 😀 |
- Go to https://workshop.colorado.edu/rstudio and login with the username and password
- We will copy the commands provided in each part (pages on the right)
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We will run the Linux commands of Part 2 (SAIGE) and Part 4 (SAIGE-GENE) in the Linux terminal within RStudio for today's workshop hands-on. The same Linux scripts can be run directly on a Linux cluster through SSH login.
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Many details about different parameters and files are provided for future reference.
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The 4 parts are independent of each other.
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The programs of the four methods have been pre-installed in the workshop cluster for the hands-on. Here are the ways to install them in your own machines for future data analyses.
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Detailed documentation of SAIGE/SAIGE-GENE can be found here https://saigegit.github.io/SAIGE-doc/