54gene Whole Genome Sequencing Germline Calling Pipeline

Documentation of WGS variant calling at 54gene

• Overview
  • Inputs
  • Outputs
• Installation
  • Obtain a copy of this workflow
  • Install the run-time environment
• Configuration
  • Configuration file
  • Manifest file
  • Intervals file
  • Sex linker file
  • MultiQC configuration
  • Config parameters
• Execution
  • Deploying the pipeline
  • Wrapper scripts
  • Automatic retries with scaling resources
  • Logging
• Investigate the results
  • Assessing completion
  • Outputs and results
  • QC
• Tests
  • Unit tests
  • Pipeline/Integration tests
  • Snakemake unit tests
  • CI/CD
• Core pipeline
  • Pulling in resources
  • FastQC and read trimming
  • Read alignment, deduplication, and BQSR
  • Variant calling
  • Joint genotyping
  • Variant filtering
  • Post-calling QC
• Changelog
  • [1.0.0] - 2022-08-01
• For developers
  • Contribute back
  • Obtain updates from upstream
• References