New Fugue - Revision history

Welchr: /* Download */

2010-09-27T17:35:06Z

Download

← Older revision		Revision as of 13:35, 27 September 2010
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	yum install zlib-devel		yum install zlib-devel

			If yum is not installed, you can try the following:

			sudo apt-get install zlib1g-dev

	== References ==		== References ==

	Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67		Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67

Goncalo: /* Download */

2010-09-27T16:48:07Z

Download

← Older revision		Revision as of 12:48, 27 September 2010
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	== Download ==		== Download ==

	A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-06-02.tar.gz source tar-ball].		A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-06-02.tar.gz source tar-ball]. After downloading, you should unpack the archive using <code>tar</code> and run <code>make</code> to compile and install <code>new_fugue</code>. Typically, that should work like this:

			tar -zxvf generic-new_fugue-2010-06-02.tar.gz
			cd generic-new_fugue
			make all
			make install

			In some systems, notably those based on Ubuntu, you might see an error message complaining that zlib is missing. [[zlib]] is required for
			new_fugue to handle compressed files. If you have administrative privileges on your machine, you will want to install zlib using the <code>yum</code> package manager. The command line will look like this:

			yum install zlib-devel

	== References ==		== References ==

	Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67		Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67

Goncalo: /* Download */

2010-06-02T17:22:03Z

Download

← Older revision		Revision as of 13:22, 2 June 2010
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	== Download ==		== Download ==

	A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-05-25.tar.gz source tar-ball].		A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-06-02.tar.gz source tar-ball].

	== References ==		== References ==

	Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67		Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67

Goncalo: /* Linkage Disequilibrium File Options */

2010-05-25T15:05:27Z

Linkage Disequilibrium File Options

← Older revision		Revision as of 11:05, 25 May 2010
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	; --minrsq		; --minrsq
	: only record markers that have rsq greater than a specific threshold		: only record markers that have rsq greater than a specific threshold

			== X Chromosome Analyses ==

			Use the <code>new_fugueX</code> executable.

	== Download ==		== Download ==

Goncalo: /* Command Line Options */

2010-05-25T15:04:37Z

Command Line Options

← Older revision		Revision as of 11:04, 25 May 2010
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	'''New Fugue''' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described by Abecasis and Wigginton (2005) and originally implemented in the [http://www.sph.umich.edu/csg/abecasis/Merlin Merlin package].		'''New Fugue''' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described by Abecasis and Wigginton (2005) and originally implemented in the [http://www.sph.umich.edu/csg/abecasis/Merlin Merlin package].

	== Command Line Options ==		= Command Line Options =

	=== Input Files ===		== Input Files ==

	; -d ''datafile''		; -d ''datafile''
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	: Output file prefix.		: Output file prefix.

	=== Frequency Estimates ===		== Frequency Estimates ==

	; --alleles		; --alleles
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	: Estimate maximum likelihood haplotype frequencies		: Estimate maximum likelihood haplotype frequencies

	=== Linkage Disequilibrium Estimates ===		== Linkage Disequilibrium Estimates ==

	; --diseq		; --diseq
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	: Only report linkage disequilibrium for marker pairs that include ''marker''		: Only report linkage disequilibrium for marker pairs that include ''marker''

	=== Linkage Disequilibrium File Options ===		== Linkage Disequilibrium File Options ==

	; --ids		; --ids
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	; --minrsq		; --minrsq
	: only record markers that have rsq greater than a specific threshold		: only record markers that have rsq greater than a specific threshold



	== Download ==		== Download ==

Goncalo at 15:04, 25 May 2010

2010-05-25T15:04:05Z

@@ Line 1: / Line 1: @@
 [[Category:Software]]
 '''New Fugue''' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described by Abecasis and Wigginton (2005) and originally implemented in the [http://www.sph.umich.edu/csg/abecasis/Merlin Merlin package].
 == Download ==

Goncalo: /* Download */

2010-05-25T14:54:07Z

Download

← Older revision		Revision as of 10:54, 25 May 2010
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	== Download ==		== Download ==

	A source file with the current distribution is available for download from this ~~link:~~ [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-05-11.tar.gz ~~generic~~-~~new_fugue-2010-05-11.tar.gz~~].		A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-05-25.tar.gz source tar-ball].

	== References ==		== References ==

	Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67		Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67

Goncalo at 17:54, 11 May 2010

2010-05-11T17:54:25Z

← Older revision		Revision as of 13:54, 11 May 2010
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	''New Fugue'' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described by Abecasis and Wigginton (2005) and originally implemented in the [http://www.sph.umich.edu/csg/abecasis/Merlin Merlin package].		[[Category:Software]]
			'''New Fugue''' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described by Abecasis and Wigginton (2005) and originally implemented in the [http://www.sph.umich.edu/csg/abecasis/Merlin Merlin package].

	== Download ==		== Download ==

Goncalo: Created page with '''New Fugue'' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described b…'

2010-05-11T13:16:00Z

Created page with '''New Fugue'' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described b…'

New page

''New Fugue'' is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described by Abecasis and Wigginton (2005) and originally implemented in the [http://www.sph.umich.edu/csg/abecasis/Merlin Merlin package].

== Download ==

A source file with the current distribution is available for download from this link: [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-05-11.tar.gz generic-new_fugue-2010-05-11.tar.gz].

== References ==

Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67