SISG Module 12: Computational Pipeline for WGS Data

2018-07-22

1 Introduction

This site contains course materials for SISG Module 12: Computational Pipeline for WGS Data, July 18-20, 2018. 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 RStudio Server at http://34.208.147.133:8787 with your username and password.

Slides for lectures are posted here below in the schedule. A detailed description of the course and instructor biographies can be found at https://www.biostat.washington.edu/suminst/SISG2018/modules/SM1812

Join the Slack channel here:
https://sisg2018module12.slack.com

1.1 Schedule

Wednesday, July 18

• Introduction
• Data formats
  • Sequencing data formats
  • Intro to Genomic Data Storage
• Population structure and relatedness
  • Population structure inference
  • Relatedness inference
  • R packages: GENESIS, SNPRelate

Thursday, July 19

• Phenotype harmonization
• Association tests
  • Methods and motivation
  • GENESIS for association tests
• Variant annotation

Friday, July 20

• Variant annotation
• Pipeline design and examples
  • Cloud computing introduction
  • Analysis pipeline design
  • Analysis pipeline on the cloud
• Cloud platforms
  • Seven Bridges Genomics
  • Analysis Commons
• Hands-on cloud computing
  • Seven Bridges exercises

1.2 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