Germline Small-Variant Annotation and Pathogenicity Classification on NCHC

This repository a VEP-based annotation and point-based in-house ACMG classification workflow for germline small variants — GRCh38.

For detailed information about this pipeline, please refer to the white paper and hands-on in this repo.

Create the environment

Use the utils/setup_env.sh file to create a conda environment.

cd utils
bash setup_env.sh

After executing this command, you can choose where to install your conda environment and caches.

Usage

1. Change the "Customize" section in config.sh.
2. Execute submit.sh.

   bash submit.sh