Population structure

Compute environment setup

If you haven’t already done so, please read Compute environment for information on how to prepare your working directory.

Learning objectives

Data setup

UPPMAX

Local

Tools

Listing

UPPMAX modules

Execute the following command to load modules:

module load uppmax bioinfo-tools ANGSD R_packages

Conda

Copy the contents to a file environment.yml and install packages with mamba env update -f environment.yml.

channels:
  - conda-forge
  - bioconda
  - default
dependencies:
  - r-base
  - angsd

Jupyter notebooks

The rendered notebook instructions are located as html files, with embedded buttons to download the actual notebooks (keep an eye out for the Download Notebook button in the top right), here:

Source: pca_mds_toy_example.ipynb

Source: pca_admixture_1000G.ipynb

Notebooks are also available for download at https://uppsala.instructure.com/courses/86976/pages/population-structure-notebooks