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Currently we support UMAKE only on Ubuntu 9.10 and later on 64-bit processors. perl (5.0 or higher) must be installed with IO::File, IO::Zlib, and Getopt::Long packages.
Currently we support UMAKE only on Ubuntu 9.10 and later on 64-bit processors. perl (5.0 or higher) must be installed with IO::File, IO::Zlib, and Getopt::Long packages.
Note that UMAKE requires external software packages to be copied to <code>$(UMAKE_HOME)/ext></code> directory
Note that UMAKE requires external software packages to be copied to <code>$(UMAKE_HOME)/ext/</code> directory
* <code>bgzip</code> and <code>tabix</code> - To download, go to [http://sourceforge.net/projects/samtools/files/tabix/ TABIX Download]
* <code>bgzip</code> and <code>tabix</code> - To download, go to [http://sourceforge.net/projects/samtools/files/tabix/ TABIX Download]
* <code>beagle</code> - To download, go to [http://faculty.washington.edu/browning/beagle/beagle.html#download BEAGLE Download]
* <code>beagle</code> - To download, go to [http://faculty.washington.edu/browning/beagle/beagle.html#download BEAGLE Download]
perl $(UMAKE_HOME)/scripts/umake.pl --conf [conf.file] --extract
perl $(UMAKE_HOME)/scripts/umake.pl --conf [conf.file] --extract
== Exercise with Example Resources
== 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.
== Software Components ==
== Software Components ==
UMAKE pipeline consists of the following software components (details TBA)
UMAKE pipeline consists of the following software components (details TBA)
* samtools-hybrid
* [samtools-hybrid]
* glfMerge
* [glfMerge]
* [[glfMultiples]]
* [glfMultiples]
* vcfPileup
* [vcfPileup]
* infoCollector
* [infoCollector]
* [[vcfCooker]]
* [vcfCooker]
* thunderVCF
* [thunderVCF]
== Acknowledgements ==
== Acknowledgements ==
UMAKE is a result from collaborative effort by Hyun Min Kang, Goo Jun, Carlo Sidore, Paul Anderson, Mary Kate Trost, Wei Chen, Tom Blackwell, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
UMAKE is a result from collaborative effort by Hyun Min Kang, Goo Jun, Carlo Sidore, Paul Anderson, Mary Kate Trost, Wei Chen, Tom Blackwell, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
