Contents
Note
The contents are being updated.
| Title | Topic | Presenter |
|---|---|---|
| 15-Sep-2025 | ||
| Population genomics in practice | PU | |
| Variant calling I | Introduction to concepts and population genetic data | PU |
| Introduction to variant calling | Short introduction to variant calling and the CLI | PU, VK, AS |
| Variant calling II | Data quality control | PU |
| Data QC | Quality control of data | PU, AS, VK |
| Variant calling III | Read mapping | PU |
| Read mapping | PU, AS, VK | |
| Variant calling IV | Workflow-based variant calling | PU |
| Variant calling | Workflow-based variant calling | PU, AS, VK |
| Variant filtering I | Basic variant filtering | PU |
| Variant filtering | Basic variant filtering following standard guidelines. | PU, AS, VK |
| 16-Sep-2025 | ||
| Recombination and linkage I | Introduction to recombination and linkage | PU |
| LD decay | Calculation of LD decay | PU, AS, VK |
| LD decay continued | PU, AS, VK | |
| Recombination and linkage II | Non-model organism variant filtering | PU |
| Genetic diversity | Summarizing genetic variation data; pi, Watterson’s theta | PU |
| Genetic diversity | pixy, vcftools | PU, AS, VK |
| Genetic diversity II | dXY, Fst, relation to trees and branch lengths, relation to recombination | PU |
| Genetic diversity | Branch length statistics | PU, AS, VK |
| 17-Sep-2025 | ||
| Selection | Population genetics of selection | PU |
| Selection | Applications | JH |
| Selection | PU, AS, JH, VK | |
| Demography | Population genetics of demography | PU |
| Demography | Applications | AS |
| Demography | PSMC | PU, AS, JH, VK |
| Demography | MSMC | PU, AS, JH, VK |
| 18-Sep-2025 | ||
| Population structure I | Introduction to theory, PCA | PU |
| Population structure I | Principal component analysis | PU, AS, VK |
| Population structure I, continued | AS | |
| Population structure II | Admixture | PU |
| Population structure II | Admixture | PU, AS, VK |
| Population structure III | f and D statistics | PU |
| Population structure III | Admixtools | PU, AS, VK |
| 19-Sep-2025 | ||
| Introduction to simulation | PU | |
| stdpopsim lab | PU, AS, VK | |
| Introduction to the coalescent | PU, JH, VK | |
| msprime / SLiM lab | ||
| Tree sequence inference | PU | |
| Introduction to tsinfer | PU, JH, VK |
Slides Slides (Google Drive) Exercises (JupyterLite) Exercises (Google CoLab)