Pairwise

This is the manual for the component SMAP relatedness pairwise of the SMAP package.

SMAP relatedness pairwise was designed to create genetic relationship matrices (pairwise) based on multi-allelic haplotypes generated by SMAP haplotype-sites or SMAP haplotype-window.

Contents:

• Scope & Usage
  • Scope
  • Integration in the SMAP workflow
  • Required input
  • Commands & options
  • Example commands
  • Output
• Feature Description
  • Setting the stage
  • Jaccard Distance
  • Information content of loci with Shared or Unique haplotypes
  • Loci with Complete Unique haplotypes
  • Loci with Partial Unique haplotypes
  • Loci with Complete Shared haplotypes
  • Loci with Partial Shared haplotypes
• How It Works
  • Sample selection, sample names, and sample order
  • Locus selection
  • Filtering for locus completeness
  • Filtering for sample completeness
  • Plot line curves
  • Estimate pairwise genetic similarities and distances
  • Calculate the locus information content
  • References
• Examples
  • Illustration
• Recommendations & Troubleshooting