Workflows

This document explains how to run the different workflows used in our project

Contents:

Contents:

• WGS BAM qc pipeline
• WES BAM qc pipeline
• BCFtools WGS variant filtering pipeline
• BCFtools WES variant filtering pipeline
• Freebayes variant filtering pipeline
• GATK variant filtering pipeline
• VCF decoration
  • Dependencies
  • How to run the pipeline
  • Pipeline output
• ML-based workflow to filter a VCF
  • Foundation of the filtering
  • USAGE
• Benchmarking with a true set
  • Dependencies
  • How to run the pipeline
  • Pipeline output
• Consensus call set generation
• Phasing pipeline
• CRAM to BAM conversion
  • Dependencies
  • How to run the pipeline
  • Pipeline output