Course Overview: The H3Africa chip is being used by the H3Africa projects to generate data that will need to be analysed. 

The course will consist of two components; a series of online lectures provided by experts in that specific domain. These are to introduce the main concepts and theory behind population genetics and GWAS. The second part of the course for selected participants will be a practical Bring Your Own Data (BYOD) workshop on the analysis of H3Africa genotyping data using the H3ABioNet GWAS and Imputation workflows.

Intended Audience: People who would like to learn more about genotyping, calling, QC and running a GWAS study for the online lectures. H3Africa project members who will be undertaking the analysis of the genotype data from the H3Africa chip, and will have data available for the practical course.

Keywords: Genetics, Genomics, Nucleic acids analysis

Skill level of training: Advanced

Credential awarded: certificate of completion

Type of training: Blended learning

Venue  of  workshop:  Online  workshop  for  4  weeks  (2-­‐3  hours  per  week),  and  face  to  face workshop at the University of Cape Town for 5 days.

Dates for the workshop: 20th August – 12th September 2018: Online lectures on Monday and Wednesday afternoon. 8th October – 12th October 2018: Face to face practical workshop (bring your own data)

Workshop organizers: Verena Ras, Paballo Chauke, Mamana Mbiyavanga, Ayton Meintjes, Suresh Maslamoney, Gerrit Botha, Shaun Aron, Sumir Panji, Scott Hazelhurst, Nicola Mulder

Application opens (online and face to face workshops): 30th July 2018

Application for the practical workshop closes: 13th August 2018

Notification date for the practical workshop: 20th August 2018 (attendance requires participation in online course) 

Link to application form:

Participation: The online lecture series is open to anyone who is interested in learning more about how to analyse genotyping chip data. The practical workshop is via competitive selection and limited to H3Africa consortium members who have or will soon receive H3Africa genotyping chip data they would like to analyse, and have attended all the online lectures.

Workshop Sponsor: H3ABioNet 

Syllabus and Tools: The online lecture series will provide an overview of GWAS studies, genotype calling, quality control of data, population structure, importance of imputation, association testing, fine mapping and further analysis. The hands on workshop will provide practical guidance on the topics above, information on the H3Africa chip, the use of the H3ABioNet GWAS and imputation workflows, Nextflow, GitHub, Plink and Genesis. Participants should work on their own array data where possible. The final day will include tools for further interpretation of GWAS results.

Prerequisites: Some basic knowledge in genetics, population genetics and GWAS for the online lectures. For the practical workshop: attendance at all the online lectures; belonging to an H3Africa project; have H3Africa genotyping data and will be undertaking analysis for the H3Africa project. Knowledge of Unix / Linux and tools used for GWAS studies such as Plink is essential, for those with no Unix experience, links to online courses will be provided to be completed prior to the workshop.

*In order to for an application to be considered to attend the hands on workshop, the potential applicants must attend all the online lectures.

Objectives: After this workshop participants should:

  • Be familiar with the steps to follow when doing a GWAS association study from getting their raw dataset, genotype calling to association testing
  • Be familiar with the use of the H3ABioNet GWAS workflow
  • Be familiar with the various steps and procedures involved in imputation
  • Be able to undertake the downstream interpretation of their results
  • Be familiar with the computational infrastructure needed to undertake a GWAS analysis 

Workshop limitations: The online lecture series will provide a foundation for conducting a GWAS study and analysing genotype array data. The practical bring your own data workshop will provide skills to analyse one’s data using the H3ABioNet GWAS and Imputation workflows based on the methods and tools used. 

Online lecture series curriculum: 

Lecture focus

List of topics to be covered in the online lectures

Computational requirements for the H3ABioNet GWAS containerized workflow

●          Installing and using Nextflow

●          Installing and using Github

●          Use of containers for packaging and running tools

●          Pulling the GWAS pipeline from Github and running it locally

Introduction to Genome Wide Association Studies (GWAS) and tests

●          An overview on GWAS studies

●          Why GWAS studies are conducted

●          Types of GWAS study designs

●          Taking samples and running on a genotyping chip

Genotype calling from an .idat file

●          What files are generated from a genotype chip (Illumina)

●          How genotypes are called

●          What clusters are and mean

●          How to tell is the calling has gone well, metrics etc


Lecture focus

List of topics to be covered in the online lectures


●     The use of manifest files, its definition and purpose

●     Tools used and examples

Quality control

●     Why is QC important

●     Going through the called files, what are they and what they look like

●     How to assess good quality calls and poor quality calls

●     What one looks to QC for with examples

●     What tools are used for QC

●     What a good quality QC files look like vs poor quality QC files

Population structure

●     Why population structure is important

●     Types of population structure (terms, concepts and definitions       e.g  cryptic, relatedness)

●     How to investigate population structure, PCA plots -­‐     GENESIS

●     Correcting for population structure

●     Tools used for population structure

●     Possible confounding effects on population structure

●     Files, format and outputs for population structure

Imputation and its importance

●     What is imputation

●     What is a reference panel

●     Why is imputation used

●     Why different reference panels matter

●     Tools to do imputation

●     Files, formats and outputs for imputation

Association testing (GWAS)

●     Types of GWAS studies (brief recap as covered in talk 1)

●     Types of association testing models and their use

●     Covariates and testing / correcting for

●     P values and correcting for multiple testing

●     Manhattan plots and other visualizations

●     Tools used for GWAS testing

●     Files, formats and outputs for GWAS testing


Training Materials Availability:









Lecture videos: