e-learning
Microbial Variant Calling
Abstract
Variant calling is the process of identifying differences between two genome samples. Usually differences are limited to single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels). Larger structural variation such as inversions, duplications and large deletions are not typically covered by “variant calling”.
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 we detect differences between a set of reads from a microorganism and a reference genome
Learning Objectives
- Find variants between a reference genome and a set of reads
- Visualise the SNP in context of the reads aligned to the genome
- Determine the effect of those variants on genomic features
- Understand if the SNP is potentially affecting the phenotype
Licence: Creative Commons Attribution 4.0 International
Keywords: Variant Analysis, gmod, jbrowse1, microgalaxy, prokaryote
Target audience: Students
Resource type: e-learning
Version: 23
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- Mapping
- Quality Control
Learning objectives:
- Find variants between a reference genome and a set of reads
- Visualise the SNP in context of the reads aligned to the genome
- Determine the effect of those variants on genomic features
- Understand if the SNP is potentially affecting the phenotype
Date modified: 2024-03-15
Date published: 2018-02-26
Contributors: Anna Syme, Simon Gladman, Torsten Seemann
Scientific topics: Genetic variation, Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis
Activity log
