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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

Schedule

All posted times are Pacific time zone. At least one break will be provided each morning and afternoon.

Monday, July 19

8:50 am Zoom session starts
9:00 am Introduction to the Command Line Interface
12:00 pm Lunch
1:00 pm Basics of Cluster Computing
2:00 pm Introduction to R
5:00 pm Zoom session ends

Tuesday, July 20

8:50 am Zoom session starts
9:00 am TBA
12:00 pm Lunch
1:00 pm What is a FASTQ file?
1:30 pm Preprocessing with HTStream
2:30 pm MultiQC
3:30 pm Mapping and Alignment
1:00 pm What is a BAM file?
2:00 pm Variants in IGG
5:00 pm Zoom session ends

Wednesday, July 21

8:50 am Zoom session starts
9:00 am Data reduction: GATK, FreeBayes, and DeepVariant
12:00 pm Lunch
1:00 pm What is a VCF file?
1:30 pm Comparison of GATK, FreeBayes, and DeepVariant results
5:00 pm Zoom session ends

Thursday, July 22

8:50 am Zoom session starts
9:00 am Data analysis: Plink, and normal association vs TDT
11:00 am Lecture TBA
12:00 pm Lunch
1:00 pm Comparison of GATK, FreeBayes, and DeepVariant results
3:00 pm Lecture TBA
5:00 pm Zoom session ends

Friday, July 23

8:50 am Zoom session starts
9:00 am Visualization in R
11:00 am Experimental Design
12:00 pm Lunch
1:00 pm Visualization in R
3:00 pm What is Bioinformatics?
5:00 pm Zoom session ends