Workshop Description

This workshop uses materials developed by the Broad Institute to teach Variant Discovery with GATK.  Attendees with no prior experience in variant calling are recommended to review all of the materials below before coming to the workshop. This early preparation will allow a focus on the specific issues of running GATK on the UCLA hoffman2 cluster rather than introducing the GATK variant calling pipeline. There will also be a focus on post variant discovery quality control steps as time allows.

Day 1

  • Hoffman2 setup
  • Laptop/local computer setup
  • GATK Primer
    • GATKwr17-01-Intro_to_Variant_Discovery.pdf
  • Start GATK Tutorial, if time
    • Variant_Discovery_Tutorial.pdf

Slide for day 1 can be found here.

Day 2

  • GATK tutorial
    • Variant_Discovery_Tutorial.pdf

Slides for day 2 can be found here.

Day 3

  • Introduction to Variant Filtering
    • GATKwr17-06-Variant_filtering.pdf
  • Hard Filtering Variants

Slides for day 3 can be found here.

Technical Requirements

Prior to the start of class, attendees should have:

  • a Hoffman2 account. To apply for an account, click here
  • Everyone is required to work through the first 14 slides for Day 1. These will guide you to setting up your laptop and your hofman2 environment. We will start the first day troubleshooting any problems with these steps.

Attendees are strongly encouraged to bring a laptop computer capable of accessing UCLA’s WiFi, and recent versions of each of the following:

Instructor

Sorel Fitz-Gibbon is an assistant researcher in the laboratory of Dr. Matteo Pellegrini. Dr. Fitz-Gibbon did her undergraduate work in Molecular, Cell and Developmental Biology at UCLA and also received her Ph.D. there, in Microbiology and Molecular Genetics. Her primary research is on the bioinformatics aspect of a project using comparative genomics of oak trees to understand adaptation in the face of environmental change.

Email: sorel@ucla.edu

Workshop Details

Prerequisites: W1, 2, or
equivalent knowledge.
Length: 3 days, 2 hrs per day
Level: Advanced
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Fall Dates

Dec. 5 – 7, 9:30 – 11:30am