Bioinformatics Training Course: SNPs to GWAS

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This course will provide an introduction to tools for SNP discovery with a focus on filtering SNP data, performing diversity/population studies, methods for the discovery of genotype-phenotype associations through genome-wide association studies (GWAS) and undertaking post-GWAS studies to define candidate genes and identify supporting evidence for their involvement in traits. Participants will learn to use stand-alone and web-based software for data analyses.


  • Overview of methods to generate SNP genotyping data (variant discovery/calling)
  • Develop skills in SNP dataset processing: filtering, graphical genotype visualization, and data manipulation
  • Conduct genetic diversity and population analyses
  • Perform genome-wide association analysis: interpreting, visualizing
  • Perform post GWAS / QTL bioinformatics analyses

Key Modules

  • Intro only: SNP discovery from NGS data
  • SNP filtering and quality control
  • Genetic diversity and population structure
  • GWAS methods and quality, interpretation and visualization
  • Post-GWAS analyses for supporting candidate gene identification

Target Audience

  • Scientists
  • Private Sector agri-business employees (large and small)
  • Students

Course Dates and Duration:

  • 16 to 18 November 2021, 2 sessions per day (2hrs each session) implemented over a period of 3 days followed by scheduled one on one sessions

Deadline: September 16, 2021

Course Fee: TBD


  • Basic R and Linux (command line)
  • Use of Galaxy, SNP-Seek and other web-based tools
  • Docker instances for local analyses