WGS/WES Pipeline

Sections:

  • WGS/WES Variant Calling Pipeline
    • Overview
    • Use Cases
    • Supported Data Types
    • When to Choose WGS vs WES
    • Design Principles
    • High-Level Workflow
    • Inputs and Outputs
    • Quality, Coverage, and QC
    • Filtering Strategy Notes
    • Reference and Resource Recommendations
    • Reproducibility & Execution
    • Data Stewardship & Compliance
    • Limitations & Non-Goals
    • What’s Next
  • Run the WGS/WES Pipeline
    • Pipeline Inputs & Layout
    • Step-by-Step Workflow
      • 1) Raw Read QC
      • 2) Adapter/Quality Trimming (optional but recommended for WES)
      • 3) Alignment to Reference
      • 4) Duplicate Marking & BQSR
      • 5) Variant Calling
      • 6) Variant Filtering
      • 7) Annotation
      • 8) Cohort-Level QC & Reports
    • Parallelization & Performance
    • WES-Specific Notes
    • Expected Outputs
    • Troubleshooting
    • Next Steps
  • Advanced Analysis
    • Trio and Family-Based Analysis
    • Joint Calling for Large Cohorts
    • Copy Number Variation (CNV) Analysis
    • Mitochondrial Variant Analysis
    • Tumor Purity Estimation & Adjustment
    • Integration and Reporting
    • Next Steps
  • Annotated Examples & Interpretation
    • Example: Tumor–Normal Variant Calling
    • Example: Tumor-Only Variant Calling
    • Example: Germline Variant Calling
  • Pipeline Structure and Containerisation
    • Modular Workflow Overview
    • Support for Germline and Somatic Calling
    • Containerisation
    • Scalability and Workflow Automation
    • Example Directory Layout
    • Best Practices for Execution
  • Stage-to-Tool Mapping With Example Commands
    • Example Commands (Bash)
    • Reproducibility Checklist
  • Case Study: ITH-aware Somatic Interpretation for WGS/WES
    • What Was Built
    • Cohort Profiling and Heterogeneity
    • Drug Screening and Response Definition
    • Expression Signatures Predicting Response
    • Mechanism of Lenvatinib Resistance & Combination Strategy
    • ITH-aware Somatic Interpretation & Recommendations
    • Limitations
  • Case Study: WES in Relapsing CLL: RPS15 Mutations and Clonal Evolution
    • What Was Built
    • Cohort Profiling and Heterogeneity
    • Genomic Profiling Methods (WES Focus)
    • Drug Screening and Response Definition
    • Expression Signatures Predicting Response
    • Mechanism of Relapse & Targeted Strategies
    • Clonal Evolution-Aware Somatic Interpretation & Recommendations
    • Limitations
  • References
    • Primary Study
    • Supporting Literature
    • Databases and Resources
WGS/WES Pipeline
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