2 min read

Module 10: Variant calling

2024-01-27

Overview

Module 10 is centered on the process of variant calling, a pivotal step in genomics that involves identifying differences between a sequenced genome and a reference sequence or among genomes within a population. This module will cover the principles of variant calling, the tools and algorithms used to detect variants, and the importance of quality control in ensuring accurate variant identification. Students will learn both the theoretical and practical aspects of calling variants from de novo assembled genomes and mapped reads. The module will also emphasize the interpretation of variant data and its application in fields such as disease research, population genetics, and evolutionary biology.

Introduction

  • The concept and significance of variant calling in genomics
  • Overview of variant types, including SNPs, indels, and structural variants
  • The role of variant calling in understanding genetic diversity and disease

Topics

Principles of Variant Calling

  • Understanding the variant calling workflow
  • The difference between germline and somatic variant calling
  • The impact of sequencing technologies and read quality on variant discovery

Variant Calling Tools and Algorithms

  • Introduction to variant callers (GATK, FreeBayes, SAMtools)
  • The use of statistical models and algorithms in variant detection
  • Comparing the performance and suitability of different variant calling tools

Variant Calling from De Novo Assemblies

  • Strategies for calling variants without a reference genome
  • Challenges and solutions in de novo variant calling

Variant Calling from Mapped Reads

  • Pre-processing steps for mapped reads before variant calling
  • Detailed walkthrough of the variant calling process using mapped data

Variant Quality Control

  • Filtering and validation of called variants
  • Understanding and interpreting quality scores and confidence metrics
  • The use of databases and in silico prediction tools for variant annotation

Labs

  • Lab 1: Variant Calling with GATK/SAMtools on Mapped Reads
  • Lab 2: Quality Control and Filtering of Variant Calls

Learning Outcomes

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

  • Describe the process of variant calling and its importance in genomics.
  • Identify different types of genetic variants and understand their potential impact.
  • Use a variety of computational tools to call variants from both de novo assemblies and mapped reads.
  • Perform quality control on variant calls to ensure data accuracy.
  • Apply variant data to various genomic research contexts and communicate the results effectively.