High Throughput Genomics Analysis
I Introduction
Workshop Info
Schedule
Pre-work
Meet Your Faculty
Compute setup
AWS and Unix Intro
II Modules
Module 1: Introduction
Lecture
Introduction to Sequencing Technologies
Introduction to HTS File Formats
Module 2: Data Visualization with IGV
Lecture
Lab
Visualization Part 1: Getting Familiar with IGV
Visualization Part 2: Inspecting SNPs, SNVs, and SVs
Visualization Part 3: Automating Tasks in IGV (Optional)
Visualization Part 4: Visualizing Long Reads
Lab Answers
Visualization Part 2: Inspecting SNPs, SNVs, and SVs
Visualization Part 4: Visualizing Long Reads
Module 3
Lecture
Lab
Module 4: Single Nucleotide Variant Calling
Lecture
Lab
Calling Variants with GATK
Investigating the SNP Calls
Filter the Variants
Adding Functional Consequence
Investigating the Functional Consequence of Variants
Adding dbSNP Annotations
Investigating the Trio (Optional)
Module 5: Structural Variant Calling
Lecture
Lab
Module 6: Genome Assembly
Lecture
Lab
Sponsors
High Throughout Genomics Analysis 2021
Module 1: Introduction
Lecture
Introduction to Sequencing Technologies
Introduction to HTS File Formats