PennCNV - Revision history

Tanthony@uab.edu: added category bioinformatics

2012-04-04T15:21:16Z

added category bioinformatics

← Older revision		Revision as of 15:21, 4 April 2012
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	[[Category:Software]]		[[Category:Software]][[Category:Bioinformatics]]

Tanthony@uab.edu: added category software

2012-04-04T14:13:47Z

added category software

← Older revision		Revision as of 14:13, 4 April 2012
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	module load penncnv/penncnv		module load penncnv/penncnv
	</pre>		</pre>


			[[Category:Software]]

Tanthony@uab.edu at 19:52, 2 April 2012

2012-04-02T19:52:36Z

← Older revision		Revision as of 19:52, 2 April 2012
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	'''Project website:''' http://www.openbioinformatics.org/penncnv/		'''Project website:''' http://www.openbioinformatics.org/penncnv/

			====Load SGE module====
	The module for the PennCNV should be loaded as:		The module for the PennCNV should be loaded as:
	<pre>		<pre>
	module load penncnv/penncnv		module load penncnv/penncnv
	</pre>		</pre>

Tanthony@uab.edu at 18:49, 2 April 2012

2012-04-02T18:49:29Z

← Older revision		Revision as of 18:49, 2 April 2012
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	PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.		PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

	Project ~~Website~~: http://www.openbioinformatics.org/penncnv/		'''Project website:''' http://www.openbioinformatics.org/penncnv/

	The module for the PennCNV should be loaded as:		The module for the PennCNV should be loaded as:

Tanthony@uab.edu: created page with generic stub

2012-03-20T14:09:43Z

created page with generic stub

New page

{{Generic_stub}}

[http://www.openbioinformatics.org/penncnv/ PennCNV] is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

Project Website: http://www.openbioinformatics.org/penncnv/

The module for the PennCNV should be loaded as:
<pre>
module load penncnv/penncnv
</pre>