Gene Annotation VCF Pipeline

This is a small pipeline that leverages Nextflow to annotates tumor somatic VCFs with gene information and variant effects. 💥

Overview 🎯

This pipeline performs the following steps:

• Normalization: Filters VCFs to include only PASS variants and normalizes them using bcftools.
• Annotation: Uses Ensembl VEP (via the official Docker container for release 112.0) to annotate variants with gene symbols, mutation consequences, and protein changes.
• Parsing: Runs a custom Python script to generate summary TSV files:
  • A complete summary of all annotations.
  • A filtered summary of protein-changing variants.

Tools & Technologies 🔧

• Nextflow: Workflow orchestration for scalability and reproducibility.
• Docker / Singularity: Uses a base Docker image, hosted on Docker Hub, as well as the official Ensembl VEP Docker image.
• bcftools & tabix: For variant normalization and VCF indexing.
• Ensembl VEP: The variant effect predictor (using the official docker://ensemblorg/ensembl-vep:release_112.0 image).
• Python & pysam: For parsing and summarizing the VEP annotations.

Getting Started 🚀

Prerequisites

• Nextflow installed.
• Singularity
• A local VEP cache directory (set as an environment variable, e.g., $VEP_CACHEDIR).

Usage

Clone the repository and run the pipeline with the following command:

nextflow run annotate-vcfs.nf --vcfs <WILDCARD-VCF-PATH> -with-singularity --vep_cachedir $VEP_CACHEDIR