iWhale

iWhale detects and annotates somatic variants from cancer Whole Exome Sequencing (WES) data to support comprehensive variant characterization.

Key Features:

• Docker integration: Encapsulates the pipeline within a Docker container to provide a consistent computational environment.
• SCons workflow management: Uses SCons to manage workflow dependencies and enable automatic resumption from the last completed step after interruptions.
• Complementary variant callers: Employs MuTect2, Strelka2, and VarScan2 for somatic variant detection.
• Unified VCF output: Consolidates outputs from the variant callers into a single Variant Call Format (VCF) file per sample.
• Variant annotation: Annotates detected variants using information from multiple reference databases for detailed characterization.

Scientific Applications:

• Somatic variant discovery in cancer WES: Identification and characterization of somatic variants from Whole Exome Sequencing data.
• Study of cancer genetics: Support for investigations into the genetic underpinnings of cancer using integrated variant calls and annotations.
• Gene prioritization: Facilitation of variant prioritization for downstream research and analysis.
• Personalized medicine: Provision of annotated somatic variant data to inform individualized therapeutic considerations.

Methodology:

Uses Docker containerization and SCons for workflow management, runs MuTect2, Strelka2, and VarScan2, consolidates caller outputs into per-sample VCF files, and annotates variants using multiple reference databases.