simulation

Simulation

Results

See results.ipynb, including

1. main figure.
2. qq plot and false positive ratio in the null simulation.
3. extended results of power.
4. association testing when the causal SNP is not typed

Steps to replicate our results

1. Clone this repository and install dependency with pip install requirements.txt. Also download MIXSCORE from here to software/ folder, so the mixscore_wrapper function in admix.py can find the mixscore executable program.
2. Prepare simulated admixed genotype. Download the simulated genotype with 1000G here and unzip it to raw_geno folder.
3. Run the snakemake pipeline with Snakefile. One may need to run the experiments in parallel to speed up.

Also see

• As an alternative to run the experiments, use our genotype simulation pipeline to simulate admixed individuals with real genotypes from 1000 Genomes project.