School of Bioinformatics · Genomics & transcriptomics
Population Genomics & GWAS
Genome-wide association studies link genetic variation to traits and disease across populations. This course teaches the full GWAS pipeline and the population-genetic thinking needed to avoid its classic errors.
Course overview
Population Genomics & GWAS starts with the population genetics that underlies every association study: allele frequencies, Hardy–Weinberg equilibrium, linkage disequilibrium and population structure, and why ignoring structure creates false associations.
You then run a GWAS from raw genotypes: rigorous sample and variant QC, principal components, imputation concepts, mixed-model association testing, Manhattan and QQ plots, heritability, fine-mapping and polygenic scores, with honest discussion of transferability across ancestries.
Learning outcomes
By the end of the course you will be able to:
- Explain allele frequencies, HWE, LD and population structure
- Perform sample and variant QC on genotype data
- Control for structure with principal components and mixed models
- Run and interpret a GWAS, including Manhattan and QQ plots
- Estimate heritability, fine-map loci and build a polygenic score
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- R for Bioinformatics or equivalent
- Linux command line
Best suited to
- Human, animal and plant geneticists
- Epidemiologists and clinicians working with genotype data
- Bioinformaticians supporting association studies
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- Allele frequencies and HWE
- Linkage disequilibrium
- Drift, selection and structure
Topics
- Call rate, heterozygosity and sex checks
- Relatedness
- Variant filters
Topics
- PCA
- ADMIXTURE
- Projection onto reference panels
Topics
- Linear and logistic models
- Mixed models with REGENIE
- Genomic inflation and QQ plots
Topics
- LD clumping and fine-mapping
- SNP heritability
- Polygenic scores and portability
Topics
- Analysis plan
- Results
- Limitations
Practical sessions and projects
Capstone project
Run and report a GWAS
Take raw genotypes through QC, structure correction and association testing to fine-mapped loci and a polygenic score, and write up the results with their limits.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Population genetics
Compute allele frequencies, HWE tests and LD decay across populations in the 1000 Genomes data.
- Genotype QC
Clean a genotype dataset and document every sample and variant removed, with the reason.
- Population structure
Infer ancestry structure and decide how many principal components to include as covariates.
- Association testing
Run a GWAS on a simulated trait with planted signals and recover them without inflation.
- After the GWAS
Fine-map the top locus and build a polygenic score, measuring how its accuracy changes across ancestries.
- Project: a reported GWAS
Deliver a GWAS report with QC, results, fine-mapping and a discussion of confounding and transferability.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- 1000 Genomes Project phase 3: Population structure and LD.IGSR (public)
- Simulated case–control and quantitative traits: Association testing with known truth.Course simulations on real genotypes
Core reading
- Purcell S et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81:559–575.
- Uffelmann E et al. (2021). Genome-wide association studies. Nature Reviews Methods Primers 1:59.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Population Genomics & GWAS, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Population Genomics & GWAS
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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