Variant Analysis - Microbial Variant Calling

Exome sequencing means that all protein-coding genes in a genome are sequenced

Questions of the tutorial:

  • How do we detect differences between a set of reads from a microorganism and a reference genome

Objectives of the tutorial:

  • 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

Resource type: Tutorial

Authors: annasyme, slugger70, tseemann

External resources:
Variant Analysis - Microbial Variant Calling https://tess.elixir-europe.org/materials/variant-analysis-microbial-variant-calling Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How do we detect differences between a set of reads from a microorganism and a reference genome Objectives of the tutorial: - 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