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Allele frequency trajectory of the CCR5Δ32 deletion

This repository contains code for the CLUES selection analysis from Tracing the evolutionary path of the CCR5delta32 deletion via ancient and modern genomes.

HAPI trajectories Ancestral path trajectories Binned frequencies

If you reuse any of this code then please cite the preprint:

Ravn, K., Cobuccio, L., Muktupavela, R.A., Meisner, J.M., Benros, M.E., Korneliussen, T.S., Sikora, M., Willerslev, E., Allentoft, M.E., Irving-Pease, E.K., Racimo, F., Rasmussen, S., 2023. Tracing the evolutionary path of the CCR5delta32 deletion via ancient and modern genomes. medRxiv https://doi.org/10.1101/2023.06.15.23290026

Installation

Download the code:

git clone [email protected]:ekirving/ccr5_paper.git && cd ccr5_paper/

The easiest way to install all the dependencies is with the conda package manager.

conda env create --name ccr5 --file environment.yaml

Then activate the environment:

conda activate ccr5

Running the HAPI analyses

These commands run the CLUES selection tests using the deletion calls from the HAPI models.

# run all the CCR5 and control models
./run_hapi_analysis.sh
# infer the ages of the alleles
Rscript scripts/infer_allele_ages.R
# plot the composite figure
Rscript scripts/plot_hapi_models.R

Running the ancestry path analyses

These commands run the CLUES selection tests using the ancestry stratified tag SNPs for the CCR5Δ32 deletion.

# run all the CCR5 and control models
./run_ancestry_analysis.sh
# plot the composite figure
Rscript scripts/plot_ancestry_models.R

Author

Evan K. Irving-Pease, GLOBE Institute, University of Copenhagen

License

This project is licensed under the MIT License - see the LICENSE file for details