A tool to simulate lcWGS MGMMs. This repository contains a Python script simulate_1x.py designed to process high-coverage whole-genome sequencing VCF files. The script takes an input VCF file and generates outputs in a directory of interest.
Clone this repository to your local machine:
git clone https://github.com/chvbs2000/lcWGS_simulation.git
cd lcWGS_simulation
Before you run the script, ensure you have Python 3.8.3 installed on your system. You can download Python 3 from the official Python website.
This project uses the following package versions:
| Package | Version |
|---|---|
| subprocess | (standard library) |
| argparse | 1.1 |
| multiprocessing | (standard library) |
| numpy | 1.22.4 |
| random | (standard library) |
| gzip | (standard library) |
| allel | 1.3.2 |
| decimal | (standard library) |
| pandas | 2.0.3 |
| os | (standard library) |
| scikit-learn | 1.3.0 |
| datetime | (standard library) |
Ensure that the listed versions are installed in your environment for compatibility. You can install the specified versions using pip with the following command:
pip install numpy==1.22.4 pandas==1.3.3 scikit-learn==0.24.2 scikit-allel==1.3.3python -m venv myenv
source myenv/bin/activate
pip install numpy==1.22.4 pandas==1.3.3 scikit-learn==0.24.2 scikit-allel==1.3.3
conda create --name myenv numpy=1.22.4 pandas=1.3.3 scikit-learn=0.24.2 scikit-allel=1.3.3
conda activate myenv
To use the script, you need to provide it with a VCF file and specify an output directory where the results will be stored. Here is the basic command structure:
python3 simulate_1x.py --input_vcf $vcf --output_dir $myoutdir
--input_vcf: The path to the input VCF file. This should be a high-coverage whole-genome sequencing VCF file, for example, NA12878.chr22.30x.vcf.gz.--output_dir: The directory where the output files will be saved. If the directory does not exist, the script will create it.
Here is an example command using a specific VCF file and output directory:
python3 simulate_1x.py --input_vcf ./demo_data/NA12878.chr22.30x.subset.vcf.gz --output_dir ./output
This command processes the VCF file NA12878.chr22.30x.subset.vcf.gz and places the output in the ./output directory. The output file in this test case will be NA12878.chr22.30x.subset.simulated.lc.vcf.gz. Make sure the output directory exist before run the code.
The script will generate a BGZF-compressed format simulated VCF files:
Ensure you have enough disk space and the necessary permissions to write to the directory.
For support, create an issue in this repository or contact the repository owner.