VaDiR

VaDiR detects somatic and expressed-gene variants from RNA sequencing datasets to enable identification and prioritization of mutations in cancer genomes.

Key Features:

• Integrated Variant Calling: VaDiR integrates three variant callers—SNPiR, RVBoost, and MuTect2—to define "Tier 1 variants" with high precision from RNA-seq data.
• Enhanced Precision and Recall: VaDiR combines Tier 1 variants with additional MuTect2 and SNPiR calls to maximize recall while maintaining precision.
• Functional Relevance: The workflow targets mutations in expressed genes to prioritize variants with potential functional impact and reduce uncertainty from non-coding or unexpressed genes.
• Orthogonal Validation Support: VaDiR supports cross-validation of sequence variations using paired RNA/DNA sequencing datasets to enhance reliability of mutation discovery.

Scientific Applications:

• Cancer Genomics: Characterizing sequence variations within actively transcribed coding regions in cancer genomes to prioritize functionally relevant mutations.
• Functional Analysis: Enabling downstream functional studies of RNA-identified variants to investigate roles in cancer progression and treatment response.

Methodology:

Analysis of RNA sequencing datasets with integration of SNPiR, RVBoost, and MuTect2 to define Tier 1 variants, and support for orthogonal validation using paired RNA/DNA sequencing datasets.