Overview

• GRG Concepts
  • GRG
  • Samples
  • Mutations
  • Missing Data
  • Unphased Data
  • Individual “Coalescences”
  • Variations of GRGs
• Installing GRGL
  • Advanced: Installing from source
• Constructing GRGs from raw data
  • Convert VCF to IGD
  • Construct GRG from IGD
  • Construct GRG from indexed VCF
  • Construct GRG from unindexed VCF
• Construct GRG via Python API
• Extra Options
  • Population Labels
• Matrix multiplication with GRG
  • Allele Frequency
  • Hamming Distance
  • Transformation of the genotype matrix
  • Whole genome (all chromosomes)
• Graph Traversals
• Converting tree-sequence (TS) to GRG
  • Mapping between TS and GRG mutations
  • A note about Mutation times
  • Node coalescence counts