Foundations Complete
Congratulations on completing the GWAS foundations
You have now completed the foundational block of the Applied GWAS guide.
This is a significant milestone.
GWAS is conceptually demanding, and reaching this point means you now understand how the pieces fit together.
What you have accomplished
By completing the foundations, you can now:
- explain what a GWAS tests and what it does not claim
- reason about study design and phenotype definition
- understand genotype and phenotype data structures
- evaluate quality control decisions and their consequences
- recognize population structure and relatedness as sources of confounding
- understand how association models are constructed and interpreted
These skills form the backbone of any serious GWAS analysis.
From understanding to application
So far, the focus has been on thinking clearly rather than running large analyses.
This was intentional.
Strong GWAS results depend more on: - sound assumptions - defensible decisions - careful interpretation
than on software commands alone.
What changes in the applied track
In the applied (premium) lessons, the emphasis shifts.
You will:
- run association analyses across many variants
- generate and interpret Manhattan and QQ plots
- explore multiple testing and power in practice
- connect statistical signals to biological questions
- work with more realistic workflows and tooling
The conceptual foundations you have built will guide every step.
A note on expectations
Applied GWAS work can be messy.
Results are often subtle.
Signals require validation.
Interpretation demands caution.
This guide will not promise shortcuts.
It will focus on building workflows and judgment you can trust.