Installation

Dependencies

External Tools

VariantCentrifuge requires several bioinformatics tools to be installed and available in your PATH:

  • bcftools - For variant extraction and manipulation

  • snpEff - For generating gene BED files and functional annotations

  • SnpSift - For filtering and field extraction

  • bedtools (specifically sortBed) - For sorting BED files

Installing via mamba/conda

mamba create -y -n annotation bcftools snpsift snpeff bedtools
mamba activate annotation

Ensure these tools are in your PATH before running VariantCentrifuge.

Python Requirements

VariantCentrifuge requires Python 3.7+ and the following Python packages:

  • pandas - For XLSX conversion and data handling

  • jinja2 - For HTML template rendering

  • openpyxl - For XLSX creation

  • scipy - For Fisher exact test in variant analysis

  • statsmodels - For multiple testing correction in gene burden analysis

Installation Methods

Method 2: Install from Source

  1. Clone the repository:

    git clone https://github.com/scholl-lab/variantcentrifuge.git
cd variantcentrifuge

  2. Set up a virtual environment (recommended):

    python3 -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

  3. Install the package:

    pip install .

    For development (editable install):

    pip install -e .

Method 3: Using conda environment

# Clone the repository
git clone https://github.com/scholl-lab/variantcentrifuge.git
cd variantcentrifuge

# Create and activate conda environment
mamba env create -f conda/environment.yml
mamba activate annotation

# Install the package
pip install -e .

Verification

Verify your installation by running:

variantcentrifuge --version

And check that external tools are available:

bcftools --version
snpEff -version
java -jar $SNPSIFT_JAR
bedtools --version

Troubleshooting

Common Issues

  1. External tools not found:

    • Ensure all external tools are installed and in your PATH

    • For conda installations, activate the correct environment

  2. Permission errors:

    • Use --user flag with pip: pip install --user variantcentrifuge

    • Or use a virtual environment

  3. Version conflicts:

    • Use a fresh virtual environment or conda environment

    • Update pip: pip install --upgrade pip

Environment Variables

You may need to set environment variables for some tools:

export SNPEFF_JAR=/path/to/snpEff.jar
export SNPSIFT_JAR=/path/to/SnpSift.jar

Next Steps

Once installed, proceed to the Usage Guide to learn how to configure and run VariantCentrifuge.