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Structural Variation Workflow

Identification of structural variants for the pharmacogenomics pipeline

The structural variation module performs the following operations:

  • Align of amplicons to the reference genome using LAST.
  • Identify split alignments
  • Summarize split alignments

Requirements

Installation

  • Clone the repository

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

  • Change to the structural_variaiton directory

    • cd structural_variation

  • Create a conda environment for running the pipeline

    • conda env create -n structural_variation -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

Pipeline configuration settings can be altered by editing config.yaml.

Execution

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