HAMLET documentation

• Installation
  • Download HAMLET
  • Setup the environment
  • Download the reference files
  • Run the test suite
• Usage
  • Input files
  • Execution
    • Snakemake profile
    • Running HAMLET
  • Output files
    • Grouping results from multiple samples
• Background
  • Citation
• Common issues
  • Using singularity
  • Snakemake errors about reserved keywords
• qc-seq module
  • Tools
  • Input
  • Output
  • Configuration
    • Example
    • Configuration options
• snv-indels module
  • Tools
  • Variant annotations
  • Input
  • Output
  • Configuration
    • Example
    • Configuration options
    • Filter and annotation criteria
    • Known variant annotations
• fusion module
  • Tools
  • Input
  • Output
  • Configuration
    • Example
    • Configuration options
• itd module
  • Tools
  • Input
  • Output
  • Configuration
    • Configuration options
• expression module
  • Tools
  • Input
  • Output
  • Configuration
    • Configuration options
    • Example
• Changelog
  • v2.5.2
  • v2.5.1
  • v2.5.0
  • v2.4.0
  • v2.3.3
  • v2.3.2
  • v2.3.1
  • v2.2.1
  • v2.1.3
  • v2.1.2
  • v2.1.1
  • v2.1.0
  • v2.0.5
  • v2.0.4
  • v2.0.3
  • v2.0.2
  • v2.0.1
  • v2.0.0