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# SISG_2023
# SISG_2024

Course materials for SISG Module 18: Computational Pipeline for WGS Data, July 26-28, 2023
Course materials for SISG Module 17: WGS Data Analysis, June 12-14, 2024

See the rendered website at
[https://uw-gac.github.io/SISG_2023](https://uw-gac.github.io/SISG_2023)
[https://uw-gac.github.io/SISG_2024](https://uw-gac.github.io/SISG_2024)
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#theme: jekyll-theme-minimal

title: SISG Module 18 | Computational Pipeline for WGS Data
title: SISG 2024 Mod 17 | WGS Data Analysis

description: July 26-28, 2023
description: June 12-14, 2024
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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](https://si.biostat.washington.edu/institutes/sisg/SM2318)** (requires login).
This site contains course materials for SISG Module 17: WGS Data Analysis, June 12-14, 2024.

- **Instructors:** Ken Rice, Laura Raffield, and Matthew Conomos
- **[Join the Slack Discussion](https://uwbiostatisticssisg.slack.com/archives/C05EAUXKLUT)**
- **Instructors:** Laura Raffield and Matthew Conomos

## Course Description
This module will provide an introduction to analyzing genotype data generated from whole genome sequencing (WGS). It will focus on extensions of standard GWAS analyses (e.g. rare-variant association tests) and “post-GWAS” follow-up analyses (e.g. conditional analysis, fine-mapping), and how WGS may improve results or be best utilized for these analyses; methods that incorporate variant annotation information will be highlighted.

Methods and examples will be informed by the instructors’ experience in large human genetics consortia (e.g. TOPMed), and, therefore, will focus on analyzing human data, but may be applicable/extendable to other organisms. A basic introduction to cloud computing will be provided, and students will perform hands-on exercises on a genomic analysis cloud platform.

### Learning Objectives
After attending this module, participants will be able to:
1. Understand how to perform association analyses for rare variants measured in WGS data using aggregate tests
2. Access variant annotation resources and understand how to incorporate annotation information into analyses to improve power and inform results
3. Understand the theory of, and how and when to perform, various “post-GWAS” follow-up analyses
4. Leverage multi-ancestry WGS data
5. Appreciate the utility of existing genomic analysis cloud platforms and get hands-on experience with cloud computing on one of these platforms

## Course Format

#### Lectures
### Lectures
Course material will be presented through lectures. Slides for lectures are linked in the schedule below.

#### Exercises
### Exercises
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](https://platform.sb.biodatacatalyst.nhlbi.nih.gov) with your username and password -- we will use this platform for 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 SISG23 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](https://biodatacatalyst.nhlbi.nih.gov/resources/cloud-credits) ($500 worth) from BioData Catalyst. Additionally, there is guidance available for [writing BioData Catalyst cloud costs into your grant proposal budget](https://bdcatalyst.gitbook.io/biodata-catalyst-documentation/written-documentation/getting-started/writing-biodata-catalyst-into-a-grant-proposal).
- 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 SISG24 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](https://biodatacatalyst.nhlbi.nih.gov/resources/cloud-credits) ($500 worth) from BioData Catalyst. Additionally, there is guidance available for [writing BioData Catalyst cloud costs into your grant proposal budget](https://bdcatalyst.gitbook.io/biodata-catalyst-documentation/written-documentation/getting-started/writing-biodata-catalyst-into-a-grant-proposal).

All of the R code and data can also be downloaded from the [github repository](https://github.com/UW-GAC/SISG_2023) 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](https://github.com/UW-GAC/SISG_2023/archive/main.zip)
All of the R code and data can also be downloaded from the [github repository](https://github.com/UW-GAC/SISG_2024) 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_2024/archive/main.zip](https://github.com/UW-GAC/SISG_2024/archive/main.zip)


## Schedule

NOTE: All times are Pacific Daylight Time (GMT-07:00)
NOTE: All times are Eastern Daylight Time (GMT-04:00)

**Wednesday, July 26th**
**Wednesday, June 12th**

| Time | Topic | Lecture | Exercises/Discussion |
| --- | --- | --- | --- |
| 1:30pm-1:40pm | Introduction | Slides | |
| 1:40pm-2:30pm | Association Tests: Background | [Slides](https://drive.google.com/file/d/1AOCXrMpmUWErQt3BhXVM1ePGOJxvgruz/view?usp=drive_link) | |
| 2:30pm-3:00pm | Getting Started with BioData Catalyst powered by Seven Bridges | [Slides](https://docs.google.com/presentation/d/1F5LznutVHVKirsvDFurh_S1aCbNHHQhCC5JPK_0_1EY/preview?slide=id.p) | |
| 1:30pm-1:35pm | Introduction | Slides | |
| 1:35pm-3:00pm | Intro to Cloud Computing for WGS Data Analysis | [Slides] | |
| 3:00pm-3:30pm | _Coffee Break_ | | |
| 3:30pm-3:50pm | Intro to Cloud Computing for WGS Analyses | [Slides](https://docs.google.com/presentation/d/1qoDoRpUvMyPtB1Y-Z9CzBHbk2wDWtsloVvD_eNDy_Uc/preview?slide=id.p) | |
| 3:50pm-5:00pm | Intro to Genomic Data Structure Format | [Slides](https://drive.google.com/file/d/1o2k1L5J961pTDNvLxlhK8cfmtUKDjuNl/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/01_gds_intro.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/01_gds_intro.html) |

| 3:30pm-5:00pm | GWAS | [Slides] | [Slides] [.html] |

**Thursday, July 27th**
**Thursday, June 13th**

| Time | Topic | Lecture | Exercises/Discussion |
| --- | --- | --- | --- |
| 8:30am-10:00am | Single Variant Association Tests | [Slides](https://drive.google.com/file/d/1AOCXrMpmUWErQt3BhXVM1ePGOJxvgruz/view?usp=drive_link) | [Slides](https://drive.google.com/file/d/1m2AT0qd04H1Z28qXlc9Miec2eGIZ22k6/view?usp=drive_link) [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/02_single_variant_tests.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/02_single_variant_tests.html) |
| 8:30am-10:00am | GWAS: Advanced Model Extenstions | [Slides] | [Slides] [.html] |
| 10:00am-10:30am | _Coffee Break_ | | |
| 10:30am-10:45am | Single Variant Association Tests (Discussion) | | |
| 10:45am-12:00pm | Population Structure and Relatedness Inference for Association Studies | [Slides](https://drive.google.com/file/d/1rbcL7R3hut5OsEpB_e8Om1gdTXdQdGoJ/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/03_pop_structure_relatedness.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/03_pop_structure_relatedness.html) |
| 10:30am-12:00pm | Leveraging Multi-Ancestry Data: Part 1 | [Slides] [.html] |
| 12:00pm-1:30pm | _Lunch Break_ | | |
| 1:30pm-1:45pm | Population Structure and Relatedness Inference (Discussion) | | |
| 1:45pm-3:00pm | Mixed Model Association Tests | [Slides](https://drive.google.com/file/d/1stIM_xknIfJUJwUl3LMJo5zNaBxv5kpD/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/04_mixed_models.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/04_mixed_models.html) |
| 1:30pm-3:00pm | Leveraging Multi-Ancestry Data: Part 2 | [Slides] [.html] |
| 3:00pm-3:30pm | _Coffee Break_ | | |
| 3:30pm-4:00pm | Mixed Model Association Tests (Discussion) |
| 4:00pm-4:45pm | R shiny Apps for Exploring Results Demo | | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/05_exploring_association_results.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/05_exploring_association_results.html) |
| 4:45pm-5:00pm | Open Q&A | | |
| 3:30pm-5:00pm | Variant Annotation: Part 1 | [Slides] | [.Rmd] [.html] |

**Friday, July 28th**
**Friday, June 14th**

| Time | Topic | Lecture | Exercises/Discussion |
| --- | --- | --- | --- |
| 8:30am-10:00am | Recent Findings and Resources for WGS Studies | [Slides](https://docs.google.com/presentation/d/1dwRILfGhTn5Yse2sP30zNLLir9RQLJKi/preview?pli=1&slide=id.p1) | |
| 8:30am-10:00am | Variant Annotation: Part 2 | [Slides] | |
| 10:00am-10:30am | _Coffee Break_ | | |
| 10:30am-12:00pm | Multiple Variant Association Tests | [Slides](https://drive.google.com/file/d/1AOCXrMpmUWErQt3BhXVM1ePGOJxvgruz/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/07_aggregate_tests.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/07_aggregate_tests.html) |
| 10:30am-12:00pm | Multi-Variant Association Tests | [Slides] [.html] |
| 12:00pm-1:30pm | _Lunch Break_ | | |
| 1:30pm-2:00pm | Multiple Variant Association Tests (Discussion) | | |
| 2:00pm-3:00pm | Variant Annotation & Annotation Explorer | Slides | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/06_annotation_explorer.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/06_annotation_explorer.html) |
| 1:30pm-3:00pm | STAAR | Slides | [.Rmd] [.html] |
| 3:00pm-3:30pm | _Coffee Break_ | | |
| 3:30pm-4:30pm | Advanced Annotation Strategies for Association Testing & STAAR Pipeline | [Slides](https://docs.google.com/presentation/d/1Apc7JrJCvwei5iaCS8O5uX9j-UUIHM46/preview?slide=id.p1) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/08_STAAR.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/08_STAAR.html) |
| 4:30pm-5:00pm | Open Q&A | | |
| 3:30pm-5:00pm | Recent Findings and Resources for WGS Analysis | [Slides] [.html] |

## R packages used

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