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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

wANNOVAR Annotation of Variants

Start Group Exercise (40 mins)

On your machine locally (or using filezilla/winscp)

Enter in the information below with your email, the sample identifier can be anything but use something helpful like chr21workshop.

Before you click submit, select the following parameters.

Now click submit. The result you see should be something like the following:

Finally, when the results are done you should get and email and you can click the link from the previous view and see the following:

Click the CSV file link for the genome summary results and take some time to go through with your group and check out the genome summary results view button to its left.


Now on the cluster:

cd /share/workshop/gwas_workshop/${USER}/plink
# Very simple script is just turning the values into a csv file for easier analysis with R uses the adjusted tdt file
python fix_tdt.py
head -1 02-CleanedTDT/tdt_21.frq.csv > tdtfrq.csv
for i in `ls 02-CleanedTDT/*.frq.csv`; do tail -n +2 "${i}" >> tdtfrq.csv; done

head -1 02-CleanedTDT/tdt_21.tdt.adjusted.csv > tdtadj.csv
for i in `ls 02-CleanedTDT/*.tdt.adjusted.csv`; do tail -n +2 "${i}" >> tdtadj.csv; done
cat master.avinput | wc -l
cat tdtadj.csv | wc -l
cat tdtfrq.csv | wc -l

Stop Group Exercise