bio-workflows-somatic-variant-pipeline

What problem does it solve?

Orchestrates end-to-end somatic variant discovery from tumor-normal paired samples, automating preprocessing, variant calling, filtering, and annotation to produce a final somatic VCF suitable for downstream analysis.

Core Features & Use Cases

• End-to-end workflow covering preprocessing (duplication marking, base quality recalibration), somatic calling with Mutect2 or Strelka2, filtering to remove artifacts and contamination, and functional annotation (Funcotator/VEP).
• Supports tumor-normal paired samples with optional tumor-only mode, panel of normals, and gnomad-based filtering for robust somatic discovery.
• Produces annotated, ready-to-analyze VCFs and summary reports for cancer genomics research and translational studies.

Quick Start

Provide tumor-normal BAMs and a reference genome to run the pipeline and produce a filtered, annotated somatic VCF.