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

2. Install Jupyter Bash kernel

pip install bash_kernel

python -m bash_kernel.install

3. Run Part 1 notebook and select Bash from the 'New' menu in the notebook interface

jupyter notebook generating_consensus_tr_genotypes.ipynb

4. Run Part 2 notebooks

jupyter notebook investigating_tr_variation.ipynb

jupyter notebook assiciation_example.ipynb