Boutros Lab call-mtSNV pipeline

• Boutros Lab call-mtSNV pipeline
• Overview
• How To Run
  • Requirements
• Flow Diagram
• Pipeline Steps
  • 1. Extract mtDNA
  • a. BAM Processing BAMQL
  • b. CRAM processing with SAMTools
  • 2. Align mtDNA with MToolBox
  • 3. Call mtSNV with mitoCaller
  • 4. Convert mitoCaller output with Mito2VCF
  • 5. Call Heteroplasmy on Paired Samples
• Inputs
  • input.yaml
  • Single Mode
  • Paired Mode
  • input.config
  • Base resource allocation updaters
• Outputs
• Testing and Validation
  • Test Data Set
  • Running Tests with NFTest
  • Validation Tool
• References
• Discussions
• Contributors
• Please see list of Contributors at GitHub.
• License