VICES - Revision history

Gzajac: /* Introduction */

2019-04-15T13:59:08Z

Introduction

← Older revision		Revision as of 09:59, 15 April 2019
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	= Introduction =		= Introduction =

	'''VICES''' is a program that jointly estimates the proportion of contaminating DNA in samples genotyped on arrays and which other samples in the study it came from.		'''VICES''' is a program that jointly estimates the proportion of contaminating DNA in samples genotyped on arrays and which other samples in the study the contaminating DNA came from.

	= Download =		= Download =

2019-04-12T17:49:49Z

VICES Example

← Older revision		Revision as of 13:49, 12 April 2019
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	~/vices/build/vices -r vices.test.report.list.txt -s vices.test.report.iids.txt -o vices.test.report.contam.txt		~/vices/build/vices -r vices.test.report.list.txt -s vices.test.report.iids.txt -o vices.test.report.contam.txt

	Expected Output _:		'''Expected Output''' in vices.test.report.contam.txt:
	Recipient_ID Estimated_contamination Sources		Recipient_ID Estimated_contamination Sources
	iid_01 0.0107758 AF:0.00351165; Donor_iid_02:0.00726419		iid_01 0.0107758 AF:0.00351165; Donor_iid_02:0.00726419

2019-04-12T17:49:27Z

VICES Example

← Older revision		Revision as of 13:49, 12 April 2019
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	'''Download Sample Files''' [[File:vices_test.zip\|vices_test.zip]]		'''Download Sample Files''' [[File:vices_test.zip\|vices_test.zip]]

	Basic Command:		'''Basic Command''' from within the directory with the example files:
	_		~/vices/build/vices -r vices.test.report.list.txt -s vices.test.report.iids.txt -o vices.test.report.contam.txt

	Expected Output _:		Expected Output _:
	_		Recipient_ID Estimated_contamination Sources
			iid_01 0.0107758 AF:0.00351165; Donor_iid_02:0.00726419
			iid_02 0.0371312 Donor_iid_01:0.0187088; Donor_iid_03:0.0184223
			iid_03 0.0791742 Donor_iid_01:0.0236221; Donor_iid_02:0.0165325; Donor_iid_08:0.0390197
			iid_04 0.0158945 AF:0.0158945
			iid_05 0.0535897 AF:0.025121; Donor_iid_04:0.0284687
			iid_06 0.0740575 AF:0.0346833; Donor_iid_04:0.0117261; Donor_iid_10:0.0276482
			iid_07 0.00551559 AF:0.00551559
			iid_08 -0.00673222 AF:-0.00673222
			iid_09 0.000255342 AF:0.000255342
			iid_10 9.90153e-05 AF:9.90153e-05
			iid_11 -0.00138426 AF:-0.00138426
			iid_12 -0.00588946 AF:-0.00588946

	= Citation =		= Citation =

2019-04-12T15:40:34Z

VICES Example

← Older revision		Revision as of 11:40, 12 April 2019
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	= VICES Example =		= VICES Example =
	~~Coming soon~~		'''Download Sample Files''' [[File:vices_test.zip\|vices_test.zip]]

			Basic Command:
			_

			Expected Output _:
			_

	= Citation =		= Citation =

2019-04-12T15:34:05Z

Installation

← Older revision		Revision as of 11:34, 12 April 2019
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	The easiest way to install VICES is to use cget as follows:		The easiest way to install VICES is to use cget as follows:
	cget install --prefix <install_prefix> gjmzajac/VICES		cget install --prefix <install_prefix> gjmzajac/VICES


	Alternatively, you can setup a dev environment cmake directly.		Alternatively, you can setup a dev environment cmake directly.

2019-04-12T15:33:47Z

Download

← Older revision		Revision as of 11:33, 12 April 2019
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	'''Ubuntu 16.04 x64 Binary''' [[File:vices_v1.0.tar.gz\|vices_v1.0.tar.gz]]		'''Ubuntu 16.04 x64 Binary''' [[File:vices_v1.0.tar.gz\|vices_v1.0.tar.gz]]

			= Installation =

			The easiest way to install VICES is to use cget as follows:
			cget install --prefix <install_prefix> gjmzajac/VICES


			Alternatively, you can setup a dev environment cmake directly.
			cd vices
			cget install -f ./requirements.txt # Install dependencies locally.
			mkdir build && cd build # Create out of source build directory.
			cmake -DCMAKE_TOOLCHAIN_FILE=./cget/cget/cget.cmake .. # Configure project with dependency paths.
			make # Build.

	= Usage =		= Usage =

2019-04-12T15:25:18Z

Download

← Older revision		Revision as of 11:25, 12 April 2019
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	'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]		'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]

	'''Ubuntu 16.04 x64 Binary''' [[vices_v1.0.tar.gz\|vices_v1.0.tar.gz]]		'''Ubuntu 16.04 x64 Binary''' [[File:vices_v1.0.tar.gz\|vices_v1.0.tar.gz]]

	= Usage =		= Usage =

2019-04-12T15:24:14Z

Download

← Older revision		Revision as of 11:24, 12 April 2019
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	'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]		'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]

	'''Ubuntu 16.04 x64 Binary''' [[~~File:~~vices_v1.0.tar.gz\|vices_v1.0.tar.gz]]		'''Ubuntu 16.04 x64 Binary''' [[vices_v1.0.tar.gz\|vices_v1.0.tar.gz]]

	= Usage =		= Usage =

2019-02-22T19:10:35Z

Download

← Older revision		Revision as of 15:10, 22 February 2019
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	'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]		'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]
	~~<!---~~
	'''Ubuntu x64 Binary''' [[File:vices_v1.0\|vices_v1.0]]		'''Ubuntu 16.04 x64 Binary''' [[File:vices_v1.0.tar.gz\|vices_v1.0.tar.gz]]
	~~--->~~

	= Usage =		= Usage =

2019-02-13T01:55:08Z

Download

← Older revision		Revision as of 21:55, 12 February 2019
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	'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]		'''ZIP archive:''' [https://github.com/gjmzajac/vices/zipball/master/ https://github.com/gjmzajac/vices/zipball/master/]
			<!---
	'''Ubuntu x64 Binary''' [[File:vices_v1.0\|vices_v1.0]]		'''Ubuntu x64 Binary''' [[File:vices_v1.0\|vices_v1.0]]
			--->

	= Usage =		= Usage =