VARAN - Local Installation Procedure

Local Installation Procedures

Variant Effect Predictor (VEP)

VEP is a tool used to determine the effect of variants (SNPs, insertions, deletions, CNVs, or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
The steps to install VEP can be found here, while DB and FASTA files can be downloaded here.
vcf2maf

vcf2maf is the tool required to convert vcf files into maf format.
All the installation info can be found here.
Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.
All the installation info can be found here.

Follow these steps to correctly install and use Varan:

Type the following command to clone the repository folder:

git clone https://github.com/bioinformatics-policlinicogemelli/Varan.git

Navigate to the Varan directory and install all the required packages (cbioimporter and oncokb-annotator):
```
cd <varan_folder_path>/Varan
bash installer.sh
```

⚠️ Depending on your Python version, you may need to modify the installer.sh script to replace pip with pip3, if necessary.

To test the installation and verify that everything is functioning correctly, run the main script varan.py with the following command:

python varan.py -h

⚠️ If any errors occur when running varan.py, please ensure that all previous steps were completed successfully without issues.