Overview

This is a documentation for quality controls that are part of CGAP pipelines.

Contents

• Docker Image
• VCF Quality Control
  • Overview
  • Definitions
    • variant types distribution
    • base substitutions
    • transition-transversion ratio
    • heterozygosity ratio
    • depth of coverage
    • mendelian errors in trio
• BAM Quality Control
  • Overview
  • Definitions
    • Mapping stats
      • Coverage