UMAKE - Revision history

Ppwhite: /* Exercise with Example Resources */

2017-02-02T15:53:30Z

Exercise with Example Resources

← Older revision		Revision as of 11:53, 2 February 2017
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	== 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.

Ppwhite: /* Download UMAKE */

2017-02-02T14:30:38Z

Download UMAKE

← Older revision		Revision as of 10:30, 2 February 2017
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	== 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 ==

Mktrost at 14:07, 14 February 2014

2014-02-14T14:07:54Z

← Older revision		Revision as of 10:07, 14 February 2014
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	{\| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" \|		{\| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" \|
	\| style="width:100%; text-align:center; color:#000;" \|		\| style="width:100%; text-align:center; color:#000;" \|
	<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">'''NOTE: The ~~latest version of~~ UMAKE pipeline is now included in [[GotCloud]] package, and ~~the current~~ documentation is outdated. Please visit [[GotCloud]] page for more details on the latest version'''</div>		<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>
	\|}		\|}

Mktrost at 18:30, 10 October 2013

2013-10-10T18:30:08Z

← Older revision		Revision as of 14:30, 10 October 2013
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	[[Category:Software\|UMAKE]]		[[Category:Software\|UMAKE]]

	'''NOTE: The latest version of UMAKE pipeline is now included in [[GotCloud]] package, and the current documentation is outdated. Please visit [[GotCloud]] page for more details on the ~~UMAKE~~'''		<!-- BANNER ACROSS TOP OF PAGE -->
			{\| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" \|
			\| style="width:100%; text-align:center; color:#000;" \|
			<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">'''NOTE: The latest version of UMAKE pipeline is now included in [[GotCloud]] package, and the current documentation is outdated. Please visit [[GotCloud]] page for more details on the latest version'''</div>
			\|}


	'''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.

Hmkang at 14:15, 9 August 2013

2013-08-09T14:15:00Z

← Older revision		Revision as of 10:15, 9 August 2013
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	[[Category:Software\|UMAKE]]		[[Category:Software\|UMAKE]]

	NOTE: The latest version of UMAKE pipeline is now included in [[GotCloud]] package, and the current documentation is outdated. Please visit [[GotCloud]] page for more details on the UMAKE		'''NOTE: The latest version of UMAKE pipeline is now included in [[GotCloud]] package, and the current documentation is outdated. Please visit [[GotCloud]] page for more details on the UMAKE'''

	'''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.

Hmkang at 14:14, 9 August 2013

2013-08-09T14:14:41Z

← Older revision		Revision as of 10:14, 9 August 2013
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	[[Category:Software\|UMAKE]]		[[Category:Software\|UMAKE]]

			NOTE: The latest version of UMAKE pipeline is now included in [[GotCloud]] package, and the current documentation is outdated. Please visit [[GotCloud]] page for more details on the UMAKE

	'''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.

Mktrost: /* Acknowledgements */

2013-01-24T20:12:44Z

Acknowledgements

← Older revision		Revision as of 16:12, 24 January 2013
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	== 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.

Lianglim: /* Build UMAKE */

2011-12-20T02:31:39Z

Build UMAKE

← Older revision		Revision as of 22:31, 19 December 2011
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	* <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)		* <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 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/		* 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 ==

Lianglim: /* Build UMAKE */

2011-12-20T02:31:19Z

Build UMAKE

← Older revision		Revision as of 22:31, 19 December 2011
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	* <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)		* <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)

	* <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)		* <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 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/		* 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/

Lianglim: /* Build UMAKE */

2011-12-20T02:31:02Z

Build UMAKE

← Older revision		Revision as of 22:31, 19 December 2011
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	* 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] (Rename "beagle.jar" to "beagle.20101226.jar" and copy it to the "ext" folder)		* <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)