VcfCooker - Revision history

Pjvh at 05:51, 31 October 2015

2015-10-31T05:51:31Z

← Older revision		Revision as of 01:51, 31 October 2015
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	[[Category:Software\|vcfCooker]]		[[Category:Software\|vcfCooker]]

	Please see [[GotCloud]] to download vcfCooker. Downloads are [[https://github.com/statgen/gotcloud/releases on github]].		Please see [[GotCloud]] to download vcfCooker. Downloads are [https://github.com/statgen/gotcloud/releases on github].

	(Updated at 2012/01/20 10:47PM)		(Updated at 2012/01/20 10:47PM)

Pjvh: add download link

2015-10-31T05:50:56Z

add download link

← Older revision		Revision as of 01:50, 31 October 2015
Line 1:		Line 1:
	[[Category:Software\|vcfCooker]]		[[Category:Software\|vcfCooker]]

	Please see [[GotCloud]] to download vcfCooker		Please see [[GotCloud]] to download vcfCooker. Downloads are [[https://github.com/statgen/gotcloud/releases on github]].

	(Updated at 2012/01/20 10:47PM)		(Updated at 2012/01/20 10:47PM)

Hmkang at 16:22, 20 November 2013

2013-11-20T16:22:38Z

← Older revision		Revision as of 12:22, 20 November 2013
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	[[Category:Software\|vcfCooker]]		[[Category:Software\|vcfCooker]]

			Please see [[GotCloud]] to download vcfCooker

	(Updated at 2012/01/20 10:47PM)		(Updated at 2012/01/20 10:47PM)

Mktrost: /* Acknowledgements */

2013-01-24T20:12:30Z

Acknowledgements

← Older revision		Revision as of 16:12, 24 January 2013
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	== Acknowledgements ==		== Acknowledgements ==

	vcfCooker is a result from collaborative effort by Hyun Min Kang, Matthew Flickinger, Matthew Snyder, Paul Anderson, Tom Blackwell, Mary Kate ~~Trost~~, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu\| hmkang@umich.edu ]] for any questions.		vcfCooker is a result from collaborative effort by Hyun Min Kang, Matthew Flickinger, Matthew Snyder, Paul Anderson, Tom Blackwell, Mary Kate Wing, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu\| hmkang@umich.edu ]] for any questions.

Hmkang: /* Current Binary Location */

2012-01-20T16:24:35Z

Current Binary Location

← Older revision		Revision as of 12:24, 20 January 2012
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	== Current Binary Location==		== Current Binary Location==

	Current binary version of vcfCooker is available at /usr/cluster/bin/vcfCooker (as in-house software).		Current binary version of vcfCooker is available at /usr/cluster/bin/vcfCooker (as an in-house software).

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

Hmkang: /* Current Binary Location */

2012-01-20T16:24:26Z

Current Binary Location

← Older revision		Revision as of 12:24, 20 January 2012
Line 7:		Line 7:
	== Current Binary Location==		== Current Binary Location==

	Current binary version of vcfCooker is available at /usr/cluster/bin/vcfCooker .		Current binary version of vcfCooker is available at /usr/cluster/bin/vcfCooker (as in-house software).

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

Hmkang at 16:22, 20 January 2012

2012-01-20T16:22:37Z

@@ Line 7: / Line 7: @@
 == Current Binary Location==
-Current binary version of vcfCooker is available at /net/fantasia/home/hmkang/sw/vcfCooker .
+Current binary version of vcfCooker is available at /usr/cluster/bin/vcfCooker .
 == Basic Usage ==
@@ Line 94: / Line 94: @@
   --mono-subset : Includes monomorphic SNPs for the subsetting
   --filt-only-subset : Use PASS-filter SNPs only for subsetting.
 == Upgrading glfMultiples outputs (v 3.3 to v 4.0)  ==
@@ Line 113: / Line 158: @@
 * AN (NumAlleles) will be added as a new INFO field
 * AB (AlleleBalance) will be added as a new INFO field (suggested by Tom Blackwell at [[Genotype_Likelihood_Based_Allele_Balance]])
 == Acknowledgements ==
 vcfCooker is a result from collaborative effort by Hyun Min Kang, Matthew Flickinger, Matthew Snyder, Paul Anderson, Tom Blackwell, Mary Kate Trost, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.

Hmkang: /* Converting between VCF/PLINK file format */

2012-01-20T16:02:28Z

Converting between VCF/PLINK file format

@@ Line 72: / Line 72: @@
   --qGeno : Assigns genotype likelihood on the VCF file with fixed quality values (useful for data integration)
-== Subsetting
+== Subsetting the VCF file ==
 == Upgrading glfMultiples outputs (v 3.3 to v 4.0)  ==

Hmkang at 15:56, 20 January 2012

2012-01-20T15:56:14Z

@@ Line 1: / Line 1: @@
 [[Category:Software|vcfCooker]]
 '''vcfCooker''' is a software that converts VCF/BED file formats in various forms. vcfCooker is currently under development, and will be publicly released soon. The current documentation contains the minimal information of currently working functions.
@@ Line 52: / Line 54: @@
                                      --maxABZ [2147483647],
                                      --maxBCS [2147483647], --keepFilter
 == Upgrading glfMultiples outputs (v 3.3 to v 4.0)  ==

Hmkang: /* Basic Usage */

2012-01-20T14:45:34Z

Basic Usage

← Older revision		Revision as of 10:45, 20 January 2012
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	The following parameters are available. Ones with "[]" are in effect:		The following parameters are available. Ones with "[]" are in effect:

	Available Options		Available Options
	Recipes : --write-bed, --write-vcf, --upgrade,		Recipes : --write-bed, --write-vcf, --upgrade,
	--summarize, --filter		--summarize, --filter, --subset
	VCF Input options : --in-vcf []		VCF Input options : --in-vcf []
	BED Input options : --in-bfile [], --in-bed [], --in-bim [],		BED Input options : --in-bfile [], --in-bed [], --in-bim [],
	--in-fam [],		--in-fam [],
	--ref [/data/local/ref/karma.ref/human.g1k.v37.fa]		--ref [/data/local/ref/karma.ref/human.g1k.v37.fa]
	Output Options : --out [./vcfCooker]		Subsetting options : --in-subset [], --mono-subset,
	Output compression Options : --plain [ON], --bgzf, --gzip		--filt-only-subset
	Filter Options : --winIndel, --indelVCF [], --minQUAL, --minMQ,		Output Options : --out [./vcfCooker], --qGeno,
	--maxDP [2147483647], --minDP, --~~maxAB~~ [100],		--print-every [10000]
	--winFFRQ, --maxFFRQ, --minNS,		Output compression Options : --plain [ON], --bgzf, --gzip
	--maxSTP [2147483647], --maxTTT [2147483647],		Genotype-level Filter Options : --minGQ, --minGD
	--minTTT [-2147483648]		Filter Options : --winIndel, --indelVCF [], --minQUAL,
			--minMQ, --maxDP [2147483647], --minDP,
			--maxABL [100], --winFFRQ, --maxFFRQ,
			--winFVAR, --merFVAR, --maxFVAR, --minNS,
			--maxSTP [2147483647],
			--maxTTT [2147483647],
			--minTTT [-2147483648], --maxSTR [100],
			--minSTR [-100], --maxSTZ [2147483647],
			--minSTZ [-2147483648], --maxCBR [100],
			--minCBR [-100], --maxQBR [100],
			--minQBR [-100], --maxCBZ [2147483647],
			--maxCSR [100], --minCSR [-100],
			--maxLQZ [2147483647],
			--minLQZ [-2147483648],
			--maxRBZ [2147483647],
			--minRBZ [-2147483648],
			--maxIOZ [2147483647],
			--minIOR [-2147483648],
			--maxIOR [2147483647],
			--maxAOZ [2147483647],
			--maxAOI [2147483647], --maxMQ0 [100],
			--maxMQ10 [100], --maxMQ20 [100],
			--minFIC [-2147483648], --minABE [-100],
			--maxABE [100], --maxLQR [100],
			--minMBR [-100], --maxMBR [100],
			--minABZ [-2147483648],
			--maxABZ [2147483647],
			--maxBCS [2147483647], --keepFilter

	== Upgrading glfMultiples outputs (v 3.3 to v 4.0) ==		== Upgrading glfMultiples outputs (v 3.3 to v 4.0) ==