A Snakemake workflow for simulating admixture and evaluating local ancestry inference programs.
- SLiM v3link
- msprime (link)
- RFMix version 2 (link)
- flare (link)
- MOSAIC (link)
- BCFTOOLS (link)
- BEAGLE (link)
- add_err (no link provided, personal program of Brian L. Browning - browning@uw.edu)
- Snakemake (link)
- conda (link)
mamba env create -f environment.yml --prefix ./env
conda env create -f environment.yml --prefix ./env
conda activate ./env
mkdir ./programs/MOSAIC
cd ./programs/MOSAIC
wget https://maths.ucd.ie/~mst/MOSAIC/MOSAIC_1.3.9.tar.gz
# within R
install.packages("programs/MOSAIC/MOSAIC_1.3.9.tar.gz")
- ./config/test.simulations.tsv
- ./config/test.ascertainents.tsv,
- ./config/test.analyses.tsv,
snakemake --configfile ./profiles/test/config.yaml --cores 11 --dry-run
snakemake --configfile ./profiles/test/config.yaml --cores 11
- ./results/reports/ (contains files with summaries of each analysis, for RMSD, R^2, QQ, etc.)
- ./results/{model_name}/{simulation_name}/{ascertainment_name}/{analysis_name}/ (contains the simulated data used as input to LAI, as well as the LAI calls and evaluations vs truth)