#                            Run programs to simulate data, align sequence, and call variants
#                            Paul VanRaden, USDA-AGIL, December 2015
#
#                            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 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
