Workshop Description (Intermediate Course)

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.

Workshop Materials

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

Slides for day 1 can be found here.

  • GATK tutorial
    • Variant_Discovery_Tutorial.pdf

Slides for day 2 can be found here.

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

Slides for day 3 can be found here.

For the Workshop slides, please click below.


Technical Requirements

Prior to the start of class, attendees should have:

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
  • 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:


Peter Scott, Ph.D., is a postdoctoral researcher in the laboratory of Dr. Brad Shaffer. He received his PhD in Ecology and Evolutionary Biology from the University of Alabama. Peter’s primary research interests lie in applying genomic methods to understand species limits and diversification, hybrid zone dynamics, and landscape and conservation genomics in reptiles and amphibians. Additionally, he is interested in investigating how to best apply and adapt modern genomic methods to non-model systems that are representative of difficult evolutionary questions (e.g. resolving relationships in recent, rapid radiations), or that push the limits of these technologies (e.g. organisms with very large genomes).




I thought the deliberate errors that they made us go through was helpful, and I thought Sorel was really good at being able to decipher the error messages that we got individually.
The overall introduction to variant calling discovery is very useful, and it provides a good start for people considering to work with it.

Workshop Details

Prerequisites: W1, W2, or
equivalent knowledge.
Length: 3 days, 2 hrs per day
Level: Intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Spring 2020 Dates

May 5, 6, and 7, 2020
1:30 PM to 4:30 PM