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[[Category:Software|UMAKE]]
[[Category:Software|UMAKE]]
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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">'''NOTE: The UMAKE pipeline is now included in [[GotCloud]] package and is no longer maintained as a separate download. Please see [[GotCloud]] instead. The documentation on this page is outdated. Please visit [[GotCloud]] page for more details on the latest version'''</div>
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'''UMAKE''' is a software pipeline to detect SNPs and call their genotypes from a list of BAM files. '''UMAKE''' pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies.
'''UMAKE''' is a software pipeline to detect SNPs and call their genotypes from a list of BAM files. '''UMAKE''' pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies.
== Download UMAKE ==
== Download UMAKE ==
To get a copy go to the [http://www.sph.umich.edu/csg/kang/umake/download UMAKE Download] download page.
To get a copy go to the [http://csg.sph.umich.edu//kang/umake/download UMAKE Download] download page.
== Build UMAKE ==
== Build UMAKE ==
* Create an "ext" folder under UMAKE_HOME (the path to the UMAKE package)
* Create an "ext" folder under UMAKE_HOME (the path to the UMAKE package)
* <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] (after compiling the source code, copy bgzip and tabix to the "ext" folder above)
(after compiling the source code, copy bgzip and tabix to the "ext" folder above)
* <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] (rename "beagle.jar" to "beagle.20101226.jar" and copy it to the "ext" folder)
* Copy <code>bgzip</code> and <code>tabix</code> to /usr/cluster/bin/ or replace "/usr/cluster/bin" with the complete path of the above "ext" folder at line 652 and 654 of umake.pl under $(UMAKE_HOME)/scripts/
* Copy the executables <code>bgzip</code> and <code>tabix</code> to /usr/cluster/bin/ OR you could replace "/usr/cluster/bin" with the complete path of the above "ext" folder at line 652 and 654 of umake.pl under UMAKE_HOME/scripts/
== Basic Usage Example ==
== Basic Usage Example ==
== Exercise with Example Resources ==
== Exercise with Example Resources ==
Example input files can be downloaded at [http://www.sph.umich.edu/csg/kang/umake/download 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://csg.sph.umich.edu//kang/umake/download 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.
* 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 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
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
* Finally, run BEAGLE/THUNDER genotype refinement using the
* Finally, run BEAGLE/THUNDER genotype refinement using the
perl $(UMAKE_HOME)/scripts/umake.pl --thunder
perl $(UMAKE_HOME)/scripts/umake.pl --thunder
* If using MOSIX nodes, change default MOSIX_PREFIX as following:
* If using MOSIX nodes, change default MOSIX_PREFIX as following:
MOS_PREFIX = mosrun -E/tmp -t -i -m 2000 # PREFIX FOR MOSIX COMMAND (BLANK IF UNUSED)
MOS_PREFIX = mosrun -E/tmp -t -i -m 2000 # PREFIX FOR MOSIX COMMAND (BLANK IF UNUSED)
== Acknowledgements ==
== Acknowledgements ==
UMAKE is a result from collaborative effort by Hyun Min Kang, Goo Jun, Carlo Sidore, Yun Li, 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, Yun Li, Paul Anderson, Mary Kate Wing, Wei Chen, Tom Blackwell, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
