VerifyIDintensity - Revision history

Gjun: /* Download verifyIDintensity */

2014-04-24T19:34:16Z

Download verifyIDintensity

← Older revision		Revision as of 15:34, 24 April 2014
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	== Download verifyIDintensity ==		== Download verifyIDintensity ==

	* [~~[File~~:~~VerifyIDintensity~~.~~tgz]~~]		* [https://github.com/gjun/verifyIDintensity GitHub repository]

	== Build verifyID intensity ==		== Build verifyID intensity ==

Gjun at 05:53, 26 February 2013

2013-02-26T05:53:04Z

← Older revision		Revision as of 01:53, 26 February 2013
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	-h, --help		-h, --help
	Displays usage information and exits.		Displays usage information and exits.

			== Reference ==

			Please cite the following paper:

			G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang, ''Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data'', American journal of human genetics doi:10.1016/j.ajhg.2012.09.004 (volume 91 issue 5 pp.839 - 848)


			== For sequence data ==

			[[VerifyBamID]] software can estimate sample contamination from aligned sequence reads and population minor allele frequency

Gjun at 18:36, 12 November 2012

2012-11-12T18:36:22Z

← Older revision		Revision as of 14:36, 12 November 2012
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	To build verifyIDintensity, run the following series of commands. You need [http://www.boost.org/ boost library] and [http://tclap.sourceforge.net/ tclap].		To build verifyIDintensity, run the following series of commands. You need [http://www.boost.org/ boost library] and [http://tclap.sourceforge.net/ tclap].
	tar xzvf verifyIDintensity.tgz
	make		$ tar xzvf verifyIDintensity.tgz
			$ make

	== Basic Usage ==		== Basic Usage ==

Gjun: Created page with 'VerifyIDintensity '''verifyIDintensity''' is a software that detects and estimates sample contamination using intensity data from Illumina genotyping array…'

2012-04-24T21:16:20Z

Created page with 'VerifyIDintensity '''verifyIDintensity''' is a software that detects and estimates sample contamination using intensity data from Illumina genotyping array…'

New page

[[Category:Software|VerifyIDintensity]]

'''verifyIDintensity''' is a software that detects and estimates sample contamination using intensity data from Illumina genotyping arrays using a mixture model.

== Download verifyIDintensity ==

* [[File:VerifyIDintensity.tgz]]

== Build verifyID intensity ==

To build verifyIDintensity, run the following series of commands. You need [http://www.boost.org/ boost library] and [http://tclap.sourceforge.net/ tclap].
tar xzvf verifyIDintensity.tgz
make

== Basic Usage ==

verifyIDintensity [-t <float>] [-m <int>] -n <int> [-b <string>] [-s <string>] -i <string> [-v] [-p] [--] [--version] [-h]

== Options ==

-t <float>, --threshold <float>
Minimum allele frequency for likelihood estimation, default is 0.01

-m <int>, --marker <int>
(required) Number of markers

-n <int>, --number <int>
(required) Number of samples

-b <string>, --abf <string>
Allele frequency file (ABF), which is a plain text file with SNP_ID and Allele_B frequency.
SNP_IDs should be sorted in the same order as the intensity file

-s <string>, --stat <string>
Statistics file (created if not exist)

-i <string>, --in <string>
(required) Input pre-computed intensity (.adpc.bin) file

-v, --verbose
Turn on verbose mode

-p, --persample
Do per-sample analysis, default is per-marker analysis

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.