• Cost also ​includes access to computer during training & Tea/coffee and a light lunch ​but excludes transport and accommodation.

  • Proof of payment or commitment to pay
    ​(i.e., Purchase Order) must be provided before date of training.


For enquiries on the programme, registration and payment details, email Dr Adeola Rotimi at RotimiA@arc.agric.za

Course O​utline

01 - 04 AUGUST 2022
Genome-wide Association Studies (GWAS) 

Course will run from 09h00 - 16h00 everyday

Dr. Magriet Van Der Nest (Coordinator; Senior Researcher: Bioinformatics) 
Dr Quentin Santana (Application Specialist: Bioinformatics)

Module content:

Day ​Content​SoftwareFacilitator

​​~ Introduction to ​GWAS;
~ Introduction to Linux and R;
~ Read Quality Check; and
~ Align reads to reference genome and variant detection.​​

FastQC & Cutadapt BWA​/Bowtie Samtools & Bedtools

​Magriet Van Der Nest
Quentin Santana


​~ Understanding Mapping​ (SAM/BAM) and VCF Output;
~ Phenotypic data;
~ Quality control of Samples, Variants and genotypes; and
~ Principal components analysis and association analysis adjusting for structure


Magriet Van Der Nest
Quentin Santana


~ Statistical models for genetic association studies GWAS analysis; ~ Normalisation for confounding caused by population stratification; 
 ~ Visualisation and interpreting GWAS results (Manhattan plot and QQ-Plot).

Web-based tools​​

Magriet Van Der Nest
Quentin Santana

​​4​~ Case study presentation
    (20-30 Minutes)

~ ​Individual analysis

​The trainee can bring their own data to analyse.

Dummy data will also be provided.

​Magriet Van Der Nest
Quentin Santana

~~~ Back to Genomics Training Programmes ~~~