HAPGEN - Revision history

Tanthony@uab.edu: added category bioinformatics

2012-04-04T15:12:54Z

added category bioinformatics

← Older revision		Revision as of 15:12, 4 April 2012
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	</pre>		</pre>

	[[Category:Software]]		[[Category:Software]][[Category:Bioinformatics]]

Tanthony@uab.edu: added category software

2012-04-04T14:01:04Z

added category software

← Older revision		Revision as of 14:01, 4 April 2012
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	module load hapgen/hapgen		module load hapgen/hapgen
	</pre>		</pre>

			[[Category:Software]]

Tanthony@uab.edu at 19:48, 2 April 2012

2012-04-02T19:48:03Z

← Older revision		Revision as of 19:48, 2 April 2012
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	'''Project website:''' https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html		'''Project website:''' https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html

			====Load SGE module====
	The HAPGEN environment module can be loaded as follows		The HAPGEN environment module can be loaded as follows
	<pre>		<pre>
	module load hapgen/hapgen		module load hapgen/hapgen
	</pre>		</pre>

Tanthony@uab.edu at 18:16, 2 April 2012

2012-04-02T18:16:48Z

← Older revision		Revision as of 18:16, 2 April 2012
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	{{Generic_stub}}		{{Generic_stub}}


	[https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html HAPGEN] is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region.		[https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html HAPGEN] is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region.
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	Command line syntax example for HAPGEN can be found by [https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html#Running_HAPGEN_top clicking here].		Command line syntax example for HAPGEN can be found by [https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html#Running_HAPGEN_top clicking here].

			'''Project website:''' https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html

	The HAPGEN environment module can be loaded as follows		The HAPGEN environment module can be loaded as follows

Tanthony@uab.edu: added links and wiki description.

2012-03-20T15:46:50Z

added links and wiki description.

← Older revision		Revision as of 15:46, 20 March 2012
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	{{Generic_stub}}		{{Generic_stub}}

	HAPGEN is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region.		[https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html HAPGEN] is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region.

	Command line syntax example for HAPGEN can be found by [~~http~~://~~www~~.stats.ox.ac.uk/~~~marchini~~/~~software~~/~~gwas/hapgen~~.html#Running_HAPGEN_top clicking here].		Command line syntax example for HAPGEN can be found by [https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html#Running_HAPGEN_top clicking here].


	The HAPGEN environment module can be loaded as follows		The HAPGEN environment module can be loaded as follows
	<pre>		<pre>
	module load hapgen/hapgen		module load hapgen/hapgen
	</pre>		</pre>

Tanthony@uab.edu: Page started

2012-03-19T14:04:44Z

Page started

New page

{{Generic_stub}}

HAPGEN is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region.

Command line syntax example for HAPGEN can be found by [http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html#Running_HAPGEN_top clicking here].

The HAPGEN environment module can be loaded as follows
<pre>
module load hapgen/hapgen
</pre>