Tracking Selection using Temporal Population Genomics Data

Authors:

Vitor A. C. Pavinato, Stéphane de Mita & Miguel de Navascués

This repository contains the implementation of a pipeline to run the simulations and to produce a reference table for the ABC-RF inference of demography and selection.

CITATION

@article {Pavinato2021.03.12.435133,
	author = {Pavinato, Vitor A. C. and De Mita, St{\'e}phane and Marin, Jean-Michel and de Navascu{\'e}s, Miguel},
	title = {Joint inference of adaptive and demographic history from temporal population genomic data},
	elocation-id = {2021.03.12.435133},
	year = {2021},
	doi = {10.1101/2021.03.12.435133},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2021/03/12/2021.03.12.435133},
	eprint = {https://www.biorxiv.org/content/early/2021/03/12/2021.03.12.435133.full.pdf},
	journal = {bioRxiv}
}

INSTALLATION

Dependencies:

• R packages moments and ROCR;
• For parallel computing you also should install: foreach, doParallel and parallel;
• SLiM 3.x
• bgzip 0.2.5 or higher
• tabix 0.2.5 or higher
• bcftools 1.6 or higher
• Python 2.7
• EggLib

USAGE

Rscript src/proof/main.R

CONFIGURATION

In the main script you should speficy the path of the above mentioned dependencies and other configurations that might be necessary (prior range, genome size, sample size, etc).