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Module 11: Variant annotation

2024-01-27

Overview

Module 11 delves into the critical process of variant annotation in bacterial genomics. Variant annotation is the step that follows variant calling, where identified variants are enriched with information about their potential effects on genes and their functions. This module will cover the principles of variant annotation, the use of tools like GATK and Snippy for annotating variants, and the interpretation of annotated data. Students will learn how to annotate genetic variants to predict their functional consequences and to understand their biological significance. Practical labs will provide hands-on experience with the variant annotation process and tools.

Introduction

  • The role of variant annotation in understanding the functional impact of genetic variation
  • Overview of the variant annotation process and its importance in genomics
  • Introduction to the tools and databases used for variant annotation

Topics

Principles of Variant Annotation

  • Defining variant annotation and its goals in the context of genomic analysis
  • The types of information added to variants during the annotation process

Variant Annotation Tools

  • Introduction to the Genome Analysis Toolkit (GATK) for variant discovery and annotation
  • Using Snippy for rapid bacterial variant calling and annotation
  • Comparison of features and use cases for different annotation tools

Annotating Variants with GATK

  • Detailed walkthrough of the variant annotation process using GATK
  • Understanding the output of GATK and interpreting the annotation data

Annotating Variants with Snippy

  • Utilizing Snippy for streamlined variant calling and annotation in bacterial genomes
  • Interpreting Snippy output and integrating it with other genomic data

Functional Prediction of Annotated Variants

  • Predicting the effects of variants on gene function and protein structure
  • Using databases such as dbSNP, ClinVar, and COSMIC for variant interpretation

Challenges in Variant Annotation

  • Addressing the complexities of variant annotation in bacterial genomes
  • Strategies for dealing with ambiguous or conflicting annotation information

Labs

  • Lab 1: Annotating Variants Using GATK
  • Lab 2: Rapid Variant Calling and Annotation with Snippy
  • Lab 3: Interpreting and Validating Annotated Variant Data

Learning Outcomes

By the end of this module, students will be able to:

  • Describe the process of variant annotation and its significance in the analysis of genomic data.
  • Use tools like GATK and Snippy to annotate genetic variants in bacterial genomes.
  • Interpret the functional implications of annotated variants using various databases and resources.
  • Assess the quality and reliability of variant annotations.
  • Address the challenges associated with annotating variants in bacterial genomics.
  • Communicate the results of variant annotation effectively in written and oral formats.