e-learning
Pangenome variant calling with DeepVariant
Abstract
Pangenomes reduce the limitations associated with linear reference genomes, also known as reference bias, so more reads are mapped and fewer reads get discarded. To learn more about pangenomics, please refer to this tutorial. Due to the increased natural genomic variation in pangenomes, reads can be mapped with an increased alignment accuracy, which in turn can improve downstream analysis.
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 can reads be mapped to a pangenome?
- How can DeepVariant be used to call variants?
Learning Objectives
- Mapping reads to a pangenome
- Calling variants with DeepVariant
Licence: Creative Commons Attribution 4.0 International
Keywords: Variant Analysis, pangenome
Competency level: •• Intermediate
Target audience: Students
Resource type: e-learning
Version: 1
Status: Active
Prerequisites:
- Calling variants in non-diploid systems
- Introduction to Galaxy Analyses
- Introduction to Variant analysis
- Mapping
- Pangenome analysis with Roary
- Quality Control
Learning objectives:
- Mapping reads to a pangenome
- Calling variants with DeepVariant
Date modified: 2026-09-30
Date published: 2026-09-30
Authors: 
Niklas Mayle, Saim Momin
Contributors: Tristan Reynolds
Scientific topics: Genetic variation
Activity log
