e-learning
Variant Calling Workflow
Abstract
In this tutorial we are working with files from a long-term evolution study of an E. coli population (designated Ara-3). We will perform variant calling to see how the population changed over time. We care how this population changed relative to the original population, E. coli strain REL606. Therefore, we will align each of our samples to the E. coli REL606 reference genome, and see what differences exist in our reads versus the genome.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How do I find sequence variants between my sample and a reference genome?
Learning Objectives
- Understand the steps involved in variant calling.
- Describe the types of data formats encountered during variant calling.
- Use command line tools to perform variant calling.
Licence: Creative Commons Attribution 4.0 International
Keywords: Foundations of Data Science
Target audience: Students
Resource type: e-learning
Version: 7
Status: Active
Learning objectives:
- Understand the steps involved in variant calling.
- Describe the types of data formats encountered during variant calling.
- Use command line tools to perform variant calling.
Date modified: 2023-10-23
Date published: 2022-07-07
Contributors: Fotis E. Psomopoulos, Helena Rasche, Saskia Hiltemann, Sofoklis Keisaris, The Carpentries
Scientific topics: Software engineering
Activity log
