Quick Start

• 1. Clindet
  • 1.1. Introduction
  • 1.2. Pipeline overview
  • 1.3. Steps
  • 1.4. Usage
  • 1.5. Credits
• 2. Setup Clindet
  • 2.1. install conda, Docker and SingularityCE
  • 2.2. Install Clindet
• 3. Use case
• 4. clindet workflow
  • 4.1. Small variants (SNVs/Indels) (Somatic)
  • 4.2. SNPs and small indels (Germline)
  • 4.3. Structural variants
  • 4.4. Copy Number Variants
  • 4.5. RNA-seq
  • 4.6. MultiQC
  • 4.7. Coverage
  • 4.8. Reports
  • 4.9. Key cancer genes
  • 4.10. Snakemake Rules