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      Genome-Wide Association Studies

Introduction and Lectures
Intro to the Workshop and Core
Dr. Anthony Musolf Talk
What is Bioinformatics/Genomics?
Cheat Sheets
Software and Links
Logging In
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
Closing thoughts
Workshop Photos
Github page
Biocore website

Closing Thoughts

Be Consistent

Prerequisites for bioinformatics

The bottom line

Next Steps

My recommendation is to follow all of the instructions again, from the beginning on your own and use the slack channel to ask questions or send emails to training.bioinformatics@ucdavis.edu. We will try be responsive to answering questions.

You’ll have access to the Computing Workshop resources for an additional week, use it to repeat the workshop materials, run freebayes, deepvariant, and/or work on your own dataset. Just transfer your data to /share/workshop

workshop ACTIVE 2021-07-18T00:00:00 2021-07-31T00:00:00 13-00:00:00 fleet-[18,20,28]

Upcoming Workshops

Check out our upcoming course offerings!

Previous Workshops available online

If you would like to take a look at the documentation from previous workshops.


Contact us at training.bioinformatics@ucdavis.edu

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