#                                  Run programs to simulate data, align sequence, and call variants
#                                  Paul VanRaden, USDA-AGIL, December 2015
#
#                                  Simulate pedigree (not needed if real or no pedigree is used)
# pedsim >output.pedsim
#                                  Simulate variant locations (not needed if actual locations known)
  markersim >output.markersim
#                                  Simulate reference map (not needed if real map is used)
  mapsim >output.mapsim
#                                  Hash and store reference map and known sequence variants
  storemap >output.storemap
#                                  Simulate genotypes and haplotypes of pedigree animals (not required)
# genosim >output.genosim
#                                  Simulate sequence segments (not needed if using actual sequence)
  map2seq >output.map2seq
#                                  Align sequence segments to map
  findmap >output.findmap
#                                  Summarize variant calls from findmap
  findvar >output.findvar
#                                  Test accuracy of variant calls from findvar and findmap
# sas testvar
#                                  Impute genotypes from read counts
# findhap4 >output.findhap4
#                                  Test accuracy of imputed genotypes
# sas correctSNPcheck
