/genotyping_repeats_tutorial

Code and documents

Primary LanguageJupyter Notebook

Tutorial for genotyping STRs from next-generation sequence data

Part 1 notebook.ipynb is supposed to b run first followed by Part 2 notebook.ipynb

To follow the instructions for the tutorial, run the commands below

  1. Clone the repository using
git clone https://github.com/Tandem-Repeats-Analysis-WG/genotyping_repeats_tutorial.git
  1. Install Jupyter Bash kernel
pip install bash_kernel

python -m bash_kernel.install
  1. Run Part 1 notebook and select Bash from the 'New' menu in the notebook interface
jupyter notebook generating_consensus_tr_genotypes.ipynb
  1. Run Part 2 notebooks
jupyter notebook investigating_tr_variation.ipynb

jupyter notebook assiciation_example.ipynb