MAPpoly_vignettes

Vignettes and Scripts for MAPpoly

This repository was created to host vignettes and scripts to perform polyploid genetic analysis, mostly using MAPpoly.

Vignettes

• Building a genetic map in an hexaploid full-sib population using MAPpoly
• Building a genetic map using potato genotype data from SolCAP
• Dataset examples
  • Hexaploid sweetpotato VCF dataset (Beauregard x Tanzania) obtained using VCF2SM
  • Hexaploid simulation with dosage call in MAPpoly format
  • Hexaploid simulation with dosage probabilities in MAPpoly format
  • Tetraploid potato with dosage call in MAPpoly format
  • Tetraploid potato with dosage call in CSV format
  • Tetraploid potato with dosage probabilities in MAPpoly format

Scripts

• SuperMASSA genotype probabilities using R (as proposed by Serang et al. (2012)
• MAPpoly test script