metapipeline-DNA

• metapipeline-DNA
• Overview
• How To Run
• Flow Diagram
• Pipeline Steps
  • 1. convert-BAM2FASTQ
  • 2. align-DNA
  • 3. calculate-targeted-coverage
  • 4. recalibrate-BAM
  • 5. generate-SQC-BAM
  • 6. call-gSNP
  • 7. call-sSNV
  • 8. call-mtSNV
  • 9. call-gSV
  • 10. call-sSV
  • 11. call-sCNA
  • 12. call-SRC
• Configuration
  • WGS global job submission params - UCLAHS-CDS
  • Pipeline selection
  • Pipeline-specific params
  • Intervals
  • Sample modes
  • Single
  • Paired
  • Multi
• Inputs
  • Input BAM
  • Input FASTQ
  • Input SRC
  • Mixed input
  • CNA
  • SNV
  • Input VCF
• Outputs
• Discussions
• Contributors
• References
• License