Statistical Genetics Playground

This is my playground repo for my learning process of statistical genetics. Here, I focus on trying to complete a typical stack of stats related task. Classical tasks from the basics (Quality control, pruning) to the more complex ones (gwas, population stratification, ancestry, PRS) are part of this repository notebooks,

Frameworks and Tools

1. PLINK
2. R
3. Hail (Python)

Topics

1. Basics of Plink (URL)
2. GWAS
   • QC in Python (All of Us' example)
   • Population stratification in Hail (All of Us' example)
3. Estimating global genetic ancestry using Bigsnpr package and UK Biobank
   • Ancestry proportions from allele frequencies only (Part 1)
   • Individual-level ancestry proportions from genotyped data (Part 2)
   • Create your own 23 and Me ancestry map (Part 3)
4. Polygenic risk scores (PRS)
   • QC (Part 1)
   • C+T (Part 2)