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