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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 Format

Expand All @@ -13,56 +12,47 @@ Many of the lectures will be followed with hands-on exercises. Students are enco

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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