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Mastering genomic data in population and association studies - week 44


The purpose of the course is for students to learn how to carry out basic and advanced genomic SNP data analyses, including data management (which is required by grant providers), GWAS, population stratification, Identity by descent, linkage disequilibrium, and more using PLINK – one of the most popular programs in genomics. We will also discuss common file formats (PLINK, VCF, etc.). This is a computational course, but no prior knowledge in programming is required. Students will receive a step-by-step tutorials and literature. The course will include hands-on exercises and a paper discussion.



High-throughput sequencing technologies have allowed researchers to detect variation at the individual, population, and species levels, which is the primary object of study for population genomics. However, the large amount of sequencing data brings new computational and analytical challenges to researchers. How to remove\merge\update SNPs or samples without risking an error? How can we calculate HW equilibrium, PCA, or GWAS? With PLINK, large data sets comprising thousands of SNPs genotyped for thousands of individuals can be rapidly and accurately manipulated and analyzed in their entirety. PLINK is a versatile program that supports data management, quality control, and common statistical computations on matrices of genomic variant calls, in a computationally efficient manner. PLINK is a must tool for anyone dealing with genetic information.


At the end of the course, the students will be able to:

• Describe what a variant calling file (VCF) format is and how to manage those files (Days 1-2).

• How to convert data to different formats and calculate linkage disequilibrium (Days 1-2).

• How to manipulate genomic data and calculating summary statistics (Days 1-3).

• How to investigate population structure with PLINK (Day 4).

• How to carry out genome wide association studies (GWAS) (Day 5).


More information

Dr. Zebin Zhang (

Dr. Eran Elhaik (


Apply directly to the course leader Zebin Zhang at:

Places will be filled on a first come, first served basis.

Last day for application 16 October 2022.