This site contains course materials for SISG Module 18: Computational Pipeline for WGS Data, July 26-28, 2023. Course evaluations and certificates of completion will be available via the official SISG course web page (requires login).
Course material will be presented through lectures. Slides for lectures are linked in the schedule below.
Many of the lectures will be followed with hands-on exercises. Students are encouraged to work through the exercises together. Afterwards, the instructors will walk through the exercises and lead a discussion.
To run the exercises, log into NHLBI BioData Catalyst powered by Seven Bridges with your username and password – we will use this platform for live demonstrations during the course.
All of the R code and data can also be downloaded from the github repository from which the site is built and run on your local machine. Download the complete workshop data and exercises: https://github.com/UW-GAC/SISG_2023/archive/main.zip
NOTE: All times are Pacific Daylight Time (GMT-07:00)
Wednesday, July 26th
| Time | Topic | Lecture | Exercises/Discussion |
|---|---|---|---|
| 1:30pm-1:40pm | Introduction | Slides | |
| 1:40pm-2:30pm | Association Tests: Background | Slides Recording | |
| 2:30pm-3:00pm | Getting Started with BioData Catalyst powered by Seven Bridges | Slides Recording | |
| 3:00pm-3:30pm | Coffee Break | ||
| 3:30pm-3:50pm | Intro to Cloud Computing for WGS Analyses | Slides Recording | |
| 3:50pm-5:00pm | Intro to Genomic Data Structure Format | Slides Recording | .Rmd .html |
Thursday, July 27th
| Time | Topic | Lecture | Exercises/Discussion |
|---|---|---|---|
| 8:30am-10:00am | Single Variant Association Tests | Slides Recording | Slides .Rmd .html |
| 10:00am-10:30am | Coffee Break | ||
| 10:30am-10:45am | Single Variant Association Tests (Discussion) | Recording | |
| 10:45am-12:00pm | Population Structure and Relatedness Inference for Association Studies | Slides Recording | .Rmd .html |
| 12:00pm-1:30pm | Lunch Break | ||
| 1:30pm-1:45pm | Population Structure and Relatedness Inference (Discussion) | Recording | |
| 1:45pm-3:00pm | Mixed Model Association Tests | Slides Recording | .Rmd .html |
| 3:00pm-3:30pm | Coffee Break | ||
| 3:30pm-4:00pm | Mixed Model Association Tests (Discussion) | Recording | |
| 4:00pm-4:45pm | R shiny Apps for Exploring Results Demo | Recording | .Rmd .html |
| 4:45pm-5:00pm | Open Q&A |
Friday, July 28th
| Time | Topic | Lecture | Exercises/Discussion |
|---|---|---|---|
| 8:30am-10:00am | Recent Findings and Resources for WGS Studies | Slides Recording | |
| 10:00am-10:30am | Coffee Break | ||
| 10:30am-12:00pm | Multiple Variant Association Tests | Slides Recording | Slides .Rmd .html |
| 12:00pm-1:30pm | Lunch Break | ||
| 1:30pm-2:00pm | Multiple Variant Association Tests (Discussion) | Recording | |
| 2:00pm-3:00pm | Variant Annotation & Annotation Explorer | Slides Recording | .Rmd .html |
| 3:00pm-3:30pm | Coffee Break | ||
| 3:30pm-4:30pm | Advanced Annotation Strategies for Association Testing & STAAR Pipeline | Slides | .Rmd .html |
| 4:30pm-5:00pm | Open Q&A |
A detailed tutorial and relevant R scripts for STAAR pipeline are available at https://github.com/xihaoli/STAARpipeline-Tutorial.
If you are new to R, you might find the following material helpful: