UC Davis Bioinformatics Core July Alliance for Global Health Makerere University Workshop - Variant Analysis

With the Center for Emerging and Neglected Diseases (CEND), UC Berkeley

UC Davis Genome Center Bioinformatics Core

Welcome

Genomics A Perspective

Software used in the workshop

Introductory Command line and cluster

• Intro to command-line

Intro to R and RStudio

• Getting Started
• Intro to R

  EXTRA

• Prepare Data in R
• Data in R

Data Reduction

• Files and Filetypes
• Project Setup
• Preprocessing Data
• Alignment

Variant Calling

• Variant Calling with Freebayes
• Annotation with snpEff
• Variant Manipulation in R

Analysis

Closing thoughts

Cheat Sheets

Cheat Sheets