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      Genome-Wide Association Studies

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
Dr. Anthony Musolf Talk
What is Bioinformatics/Genomics?
Support
Slack
Zoom
Cheat Sheets
Software and Links
Scripts
Prerequisites
Logging In
CLI
R
Cluster Computing
Data Reduction
Files and Filetypes
Project setup
Preprocessing raw data
Alignment with BWA
Variant calling using GATK
Comparison of freebayes, GATK, and deepvariant output
Data Analysis
Plink Step by Step TDT
Plink Step by Step TDT (solutions)
wAnnovar Annotation
Plink Step by Step (Non FBAT excercise)
Setup in R
GWAS Visualization
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

All documentation for the workshop is best viewed from the github.io pages

Documentation

Genome Wide Association Studies

Jul. 19, 2021 - Jul. 23, 2021, 9 a.m. - 5:00 p.m daily. Online learning

Contact - UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

Learn to execute a successful GWAS experiment from design to analysis. This five-day online workshop will cover experimental design, data generation, and analysis on the command line. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services. Exercises will be performed on the command line with provided datasets.

To get the most out of this course, please complete the prerequisite material in command line and R before the course, and contact us with any questions.

This workshop will be held online from 9:00 am to 5:00 pm each day.

Participants must have access to a computer with a reliable connection to the internet, current versions of R version 4.0 and Rstudio installed, and an application that allows them to ssh into a server (e.g. Bash for Windows, or Terminal for Apple).

FAQ

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … To get the most out of this course, please complete the prerequisite material in command line and R before the course, and contact us with any questions.

What do I need to bring? … Participants must have access to a computer with a reliable connection to the internet, current versions of R version 4.0 and Rstudio installed, and an application that allows them to ssh into a server (e.g. Bash for Windows, or Terminal for Apple).

Can I bring my own data? … We will provide datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How much does it cost? … The registration fee is $1,000 for current students, postdocs, staff and faculty at Univeristy of California campus’ or UC National Labs (LBNL, LANL, LLNL), $1,200 for other academic or non-profit participants and $1,700 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.

How do I apply? … All registration is “first-come, first-served”. There is no application process. So, sign up as soon as possible to ensure your place in the workshop.

Where can I find more information, including your policies? … Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.

Questions

If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu

Register

Register for the course