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
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Clone the repository
git clone https://github.com/lumc-pgx/variant_effects.git
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Change to the variant_calling directory
cd variant_effect
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Create a conda environment for running the pipeline
conda env create -n variant_effects -f environment.yaml
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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
The pipeline configuration settings are specified in config.yaml.
Edit the configfile with run-specific paths and settings.
- 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