SISG Module 17 | Computational Pipeline for WGS Data

This site contains course materials for SISG Module 17: Computational Pipeline for WGS Data, July 27-29, 2022. Course evaluations and certificates of completion will be available via the official SISG course web page (requires login).

Instructors: Ken Rice, Laura Raffield, and Matthew Conomos
TAs: Deepti Jain and Anya Mikhaylova
Zoom Link: https://washington.zoom.us/j/91863603677
Join the Slack Discussion

Course Format

Lectures

Course material will be presented through lectures given via Zoom. Slides for lectures are linked in the schedule below, and recordings of the lectures will be posted afterwards.

Exercises

Many of the lectures will be followed with hands-on exercises. Students will be split into Zoom breakout rooms where they can 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 all live demonstrations during the course.

You will retain access to the Seven Bridges platform, including your SISG Project with all of the course materials even after the course ends. The SISG22 Workshop billing group will remain available to you for a short period of time, after which you will need to set up another payment method to run analyses. You can request pilot cloud credits ($500 worth) from BioData Catalyst. Additionally, there is guidance available for writing BioData Catalyst cloud costs into your grant proposal budget.

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_2022/archive/master.zip

Schedule

NOTE: All times are Pacific Daylight Time (GMT-07:00)

Wednesday, July 27th

Time	Topic	Lecture	Exercises/Discussion
11:30am-11:40am	Introduction	Slides, Recording
11:40am-12:30pm	Using BioData Catalyst powered by Seven Bridges	Slides, Recording
12:30pm-1:30pm	Intro to Genomic Data Structure Format	Slides, Recording	.Rmd, .html, Recording
1:30pm-1:45pm	Break
1:45pm-2:30pm	Association Tests Part I: Background	Slides, Recording

Thursday, July 28th

Time	Topic	Lecture	Exercises/Discussion
8:00am-8:50am	Association Tests Part II: Single Variant Tests	Slides, Recording
8:50am-9:45am	Single Variant Association Tests with GENESIS	Slides, Recording	.Rmd, .html, Recording
9:45am-10:15am	Break
10:15am-11:45am	Population Structure and Relatedness Inference for Association Studies	Slides, Recording	.Rmd, .html, Recording
11:45am-12:45pm	Lunch
12:45pm-2:00pm	Mixed Model Association Testing	Slides, Recording	.Rmd, .html, Recording
2:00pm-2:30pm	R shiny Apps for Exploring Results Demo	Recording 1, Recording 2	.Rmd, .html

Friday, July 29th

Time	Topic	Lecture	Exercises/Discussion
8:00am-9:00am	Association Tests Part III: Multiple Variant Tests	Slides, Recording
9:00am-9:20am	Variant Annotation for Aggregate Association Testing	Slides, Recording
9:20am-10:00am	Aggregate Association Tests with GENESIS	Slides	.Rmd, .html, Recording
10:00am-10:30am	Break
10:30am-11:15am	Annotation Explorer Demo	Recording	.Rmd, .html
11:15am-12:00pm	Advanced Annotation Strategies for Association Testing	Slides, Recording
12:00pm-1:00pm	Lunch
1:00pm-2:00pm 2:00pm-2:30pm	Recent Findings for WGS Studies Open Q&A	Slides, Recording

R packages used

Resources

NHLBI BioData Catalyst Powered by Seven Bridges

Getting Started Guide for SISG22 Module 17

A detailed tutorial and relevant R scripts for STAAR pipeline are available at https://github.com/xihaoli/STAARpipeline-Tutorial. STAAR pipeline apps will also be released soon on BioData Catalyst.

If you are new to R, you might find the following material helpful:

Introduction to R materials from SISG Module 3
Graphics with ggplot2
Data manipulation with dplyr