PTpipe

PenetranceCards, a global, community-contributed public archive of variant penetrance. PTpipe is an offline script used to update penetrance in PenetranceCards. Previous studies have shown that the accuracy of penetrance is highly dependent on the sample size(McGurk, Kathryn A et al.). We encourage researchers worldwide to share their data, process it using PTpipe, and upload it to PenetranceCards, helping to enhance the accuracy of penetrance estimates within the platform.

General Settings

Configure the 'home' path

cd /path/to/PTpipe/
vi ./config/config.yaml
home: /path/to/PTpipe

Other parameters can be automatically configured through the PTpipe_run.py script.

Pipeline Setup

PTpipe can be executed using conda environments.

Conda

This workflow can easily setup manually with the given environment file. Install Snakemake and dependencies using the command:

conda env create -f environment.yml

Enter the newly created environment with:

conda activate PTpipe

Download hg38 reference genome file.

wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

Copy to the Reference path.

cp /path/to/hg38.fa.gz /path/to/PTseeker/data/reference/hg38.fa.gz

Configure the pipeline, and then execute the Snakemake pipeline through the PTpipe_run.py script.

python PTpipe_run.py

View the pipeline's help documentation.

python PTpipe_run.py --help

More installation details can be obtained in install.sh.

Example

You can quickly get acquainted with the PTpipe pipeline by running our test data.

First, navigate to the directory where PTpipe is located.

cd /path/to/PTpipe/

If the file requires basic quality control and sample filtering, use the following command.

python PTpipe_run.py --input /path/to/PTpipe/data/Test/01_qc1.vcf.gz --base_qc --sample_filtering --samplelist /path/to/PTpipe/data/Example/Example_sample_list.txt --output /path/to/PTpipe/data/result/Test.txt

If the file requires basic quality control, use the following command.

python PTpipe_run.py --input /path/to/PTpipe/data/Test/01_qc1.vcf.gz --base_qc --output /path/to/PTpipe/data/result/Test.txt

If the file has already undergone quality control and sample filtering, then use this command.

python PTpipe_run.py --input /path/to/PTpipe/data/Test/02_qc2.vcf.gz --output /path/to/PTpipe/data/result/Test.txt

License

This project is licensed under the MIT License. See the LICENSE file for details.