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perl $(UMAKE_HOME)/scripts/umake.pl --conf [conf.file] --beagle
perl $(UMAKE_HOME)/scripts/umake.pl --conf [conf.file] --beagle
perl $(UMAKE_HOME)/scripts/umake.pl --conf [conf.file] --thunder
perl $(UMAKE_HOME)/scripts/umake.pl --conf [conf.file] --thunder
perl $(UMAKE_HOME)/scripts/umake.pl --conf [conf.file] --extract
== Exercise with Example Resouces
== Exercise with Example Resources
Example input files can be downloaded at [http://www.sph.umich.edu/csg/kang/umake/ UMAKE Download]. These example resource files includs sequence alignment files over 60 individuals from the 1000 Genomes project, focusing on 300kb region in chromosome 20. Note that the reference genome FASTA file has also been modified to use chromosome 20 only.
Example input files can be downloaded at [http://www.sph.umich.edu/csg/kang/umake/ UMAKE Download]. These example resource files includs sequence alignment files over 60 individuals from the 1000 Genomes project, focusing on 300kb region in chromosome 20. Note that the reference genome FASTA file has also been modified to use chromosome 20 only.
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.
* 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
perl $(UMAKE_HOME)/scripts/umake.pl --beagle
perl $(UMAKE_HOME)/scripts/umake.pl --beagle
* Finally, run BEAGLE/THUNDER genotype refinement using the
perl $(UMAKE_HOME)/scripts/umake.pl --thunder
perl $(UMAKE_HOME)/scripts/umake.pl --thunder
* If SNP site is already defined, instead of --snpcall option, you can extract the genotype likelihood using the following command
perl $(UMAKE_HOME)/scripts/umake.pl --extract
== Preparing Your Own Input Files ==
== Preparing Your Own Input Files ==
