lai-sim

A Snakemake workflow for simulating admixture and evaluating local ancestry inference programs.

Required external 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)

create and activate a conda environment

Snakemake suggest mamba (and it is much faster, but it breaks msprime on my machine)

So I am using conda below

uses mamba, rather than conda, as suggested by Snakemake

mamba env create -f environment.yml --prefix ./env conda env create -f environment.yml --prefix ./env

activate conda environment (from base directory)

conda activate ./env

Install MOSAIC package

requires R v4

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")

dry run of the test pipeline

defined in profiles/test/config.yaml

test analyses described in:

• ./config/test.simulations.tsv
• ./config/test.ascertainents.tsv,
• ./config/test.analyses.tsv, snakemake --configfile ./profiles/test/config.yaml --cores 11 --dry-run

run the test pipeline

snakemake --configfile ./profiles/test/config.yaml --cores 11

results will be stored in:

• ./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)