VEP module for the Pharmacogenomics Pipeline

This module leverages ensembl VEP to predict the impact of genomic variants.

The variant effects module performs the following operations:

• Prediction of variant effects using ensembl VEP
• Filtering and collation of effect predictions

Requirements

• Conda/Miniconda

Installation

• Clone the repository

  • git clone https://github.com/lumc-pgx/variant_effects.git

• Change to the variant_calling directory

  • cd variant_effect

• Create a conda environment for running the pipeline

  • conda env create -n variant_effects -f environment.yaml

• In order to use the pipeline on the cluster, update your .profile to use the drmaa library:

  • echo "export DRMAA_LIBRARY_PATH=libdrmaa.so.1.0" >> ~/.profile
  • source ~/.profile

Configuration

The pipeline configuration settings are specified in config.yaml.
Edit the configfile with run-specific paths and settings.

Execution

• Activate the conda environment
  • source activate variant_effects
• For parallel execution on the cluster
  • pipe-runner --configfile config.yaml
• To specify that the pipeline should write output to a location other than the default:
  • pipe-runner --configfile config.yaml --directory path/to/output/directory