Welcome to CGAR’s documentation!

Contents:

• 1. Introduction
  • 1.1. CGAR public server
• 2. Upload Own Variant Files
  • 2.1. Browse and track previous files
• 3. Start Analysis on CGAR
  • 3.1. Publicly available samples
  • 3.2. An Example Use Case
• 4. Inside CGAR Report
  • 4.1. Genotype-based prediction of ancestral composition
  • 4.2. Side menu and main table
  • 4.3. HGMD variants
  • 4.4. ClinVar variants
  • 4.5. Genes associated with rare phenotype
  • 4.6. Putative phenotype-associated genes
  • 4.7. Secondary findings
  • 4.8. Pharmacogenomic variants
  • 4.9. User-defined set of genes
  • 4.10. De novo variant candidates
  • 4.11. Cancer-associated genes and variants
• 5. Running CGAR locally
  • 5.1. Requirements
  • 5.2. Installation
  • 5.3. Access local CGAR
  • 5.4. Source Code
• 6. Contact