SISG Module 17: Computational Pipeline for WGS Data

2019-07-25

1 Introduction

This site contains course materials for Course materials for SISG Module 17: Computational Pipeline for WGS Data, July 24-26, 2019. Data used is located in the github repository from which the site is built, as well as in the TOPMed analysis pipeline.

To work through the exercises, log into http://bit.ly/datastage-sb with your username and password.

Slides for lectures are linked below in the schedule. A detailed description of the course and instructor biographies can be found at https://www.biostat.washington.edu/suminst/SISG2019/modules/SM1917

Join the Slack channel here: https://sisg2019module17.slack.com (link to sign up)

1.1 Schedule

Wednesday, July 24

• Introduction
  • Setup for interactive exercises (Part 1)
• Sequencing data formats
  • Sequencing data formats
  • Intro to Genomic Data Storage
  • Exercises
• Phenotype harmonization
  • Exercises
• Association tests
  • Methods and motivation (Part 1)

Thursday, July 25

• Association tests
  • Methods and motivation (Part 2)
  • GENESIS for association tests
  • Exercises
  • Aggregate tests (Part 3)
  • Exercises
• Population structure and relatedness
  • Population structure inference
  • Relatedness inference
  • R packages for PCA and relatedness
  • Exercises
• Mixed model association testing
  • Exercises
• Variant annotation

Friday, July 26

• Variant annotation
  • Exercises
• Analysis pipeline on the cloud
• Cloud platforms
  • Analysis Commons
  • Seven Bridges (Part 2)
  • Terra (Account instructions)

Download the workshop data and exercises: https://github.com/UW-GAC/SISG_2019/archive/master.zip

1.2 R packages used

• SeqArray
• SeqVarTools
• GENESIS
• SNPRelate
• TopmedPipeline
• wgsaparsr
• tidyverse
• GGally

1.3 Resources

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

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