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Let <code>UMAKE_HOME</code> be the path to the UMAKE package and <code>EXAMPLE_HOME</code> be the path to the example resource files.
Let <code>UMAKE_HOME</code> be the path to the UMAKE package and <code>EXAMPLE_HOME</code> be the path to the example resource files.
* First, modify <code>UMAKE_ROOT, INPUT_ROOT, OUTPUT_ROOT</code> parameters accordingly.
* First, modify <code>UMAKE_ROOT, INPUT_ROOT, OUTPUT_ROOT</code> parameters accordingly.
* Second, perform SNP calling procedure using the following command (you need to run all commands under <code>EXAMPLE_HOME</code>)
* You need to run all commands under the <code>EXAMPLE_HOME</code> folder
* Second, perform SNP calling procedure using the following command
perl $(UMAKE_HOME)/scripts/umake.pl --snpcall
perl $(UMAKE_HOME)/scripts/umake.pl --snpcall
* Third, run BEAGLE genotype refinement using the
* Third, run BEAGLE genotype refinement using the
