Changes

* First, modify <code>UMAKE_ROOT, INPUT_ROOT, OUTPUT_ROOT</code> parameters accordingly.  

* First, modify <code>UMAKE_ROOT, INPUT_ROOT, OUTPUT_ROOT</code> parameters accordingly.  

* You need to run all commands under the <code>EXAMPLE_HOME</code> folder

* You need to run all following commands under the <code>EXAMPLE_HOME</code> folder. After each perl script is done, run the two make commands printed from the perl script.

* Second, perform SNP calling procedure using the following command  

* Second, perform SNP calling procedure using the following command  

  perl $(UMAKE_HOME)/scripts/umake.pl --snpcall

  perl $(UMAKE_HOME)/scripts/umake.pl --snpcall