VcfRefGen - Revision history

Mktrost: /* Parameter */

2014-09-04T19:53:09Z

Parameter

← Older revision		Revision as of 15:53, 4 September 2014
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	\| <code>--out <filename></code>		\| <code>--out <filename></code>
	\| Output VCF filename.		\| Output VCF filename.
			\|-
			\| <code>--allfields</code>
			\| keep info and all genotype fields and do not filter out non-phased or missing genotype genotype records.
	\|-		\|-
	\| <code>--uncompress</code>		\| <code>--uncompress</code>

2014-09-04T19:49:42Z

← Older revision		Revision as of 15:49, 4 September 2014
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	= Download =		= Download =
	Source code can in: [[Media:vcfRefGen.0.1.3.tgz‎\|VcfRefGen.0.1.3.tgz‎]] - Released 01/29/2013		Source code can in: [[Media:vcfRefGen.0.1.4.tgz‎\|VcfRefGen.0.1.4.tgz‎]] - Released 09/04/2014

			Older versions:
			* [[Media:vcfRefGen.0.1.3.tgz‎\|VcfRefGen.0.1.3.tgz‎]] - Released 01/29/2013

	= Parameter=		= Parameter=

2013-01-29T21:41:04Z

← Older revision		Revision as of 17:41, 29 January 2013
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	''vcfRefGen'' is a tool for generating VCF reference panels for [http://genome.sph.umich.edu/wiki/minimac minimac imputation]. It reduces VCF files by removing the info field, saving only the GT genotype field and removing any records where any kept sample is not phased or is missing a genotype.		''vcfRefGen'' is a tool for generating VCF reference panels for [http://genome.sph.umich.edu/wiki/minimac minimac imputation]. It reduces VCF files by removing the info field, saving only the GT genotype field (and any additional genotype fields specified in the parameters) and removing any records where any kept sample is not phased or is missing a genotype.

	= Download =		= Download =

2013-01-29T21:40:34Z

← Older revision		Revision as of 17:40, 29 January 2013
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	\| <code>--filterList <filename></code>		\| <code>--filterList <filename></code>
	\| filename of file containing regions to include. <br>format: start end <br> start & end positions should be 1-based inclusive positions <br> for SNPs start=end position		\| filename of file containing regions to include. <br>format: start end <br> start & end positions should be 1-based inclusive positions <br> for SNPs start=end position
			\|-
			\| <code>--keepGT <GTs to keep></code>
			\| comma separated list of genotype fields to keep in addition to the GT field

	\|-		\|-
	\| <code>--params</code>		\| <code>--params</code>

2013-01-29T21:19:15Z

Download

← Older revision		Revision as of 17:19, 29 January 2013
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	= Download =		= Download =
	Source code can ~~be found~~ [~~http~~:~~//www~~.~~sph~~.~~umich~~.~~edu/csg/cfuchsb/vcfRefGen~~.0.1.2.~~tgz here~~] .		Source code can in: [[Media:vcfRefGen.0.1.3.tgz‎\|VcfRefGen.0.1.3.tgz‎]] - Released 01/29/2013

	= Parameter=		= Parameter=

2013-01-24T20:12:57Z

Questions and Comments

← Older revision		Revision as of 16:12, 24 January 2013
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	== Questions and Comments ==		== Questions and Comments ==

	Please contact [mailto:cfuchsb@umich.edu Christian Fuchsberger] or [mailto:mktrost@umich.edu Mary Kate ~~Trost~~]		Please contact [mailto:cfuchsb@umich.edu Christian Fuchsberger] or [mailto:mktrost@umich.edu Mary Kate Wing]


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

2012-08-29T19:33:16Z

← Older revision		Revision as of 15:33, 29 August 2012
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	end		end
	</source>		</source>

			== Questions and Comments ==

			Please contact [mailto:cfuchsb@umich.edu Christian Fuchsberger] or [mailto:mktrost@umich.edu Mary Kate Trost]


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

2012-08-29T19:32:03Z

Download

← Older revision		Revision as of 15:32, 29 August 2012
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	= Download =		= Download =
	Source code can be found [http://www.sph.umich.edu/csg/cfuchsb/ here] .		Source code can be found [http://www.sph.umich.edu/csg/cfuchsb/vcfRefGen.0.1.2.tgz here] .

	= Parameter=		= Parameter=

2012-08-29T19:29:37Z

Example

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	runon -m 1024 vcfRefGen --in ALL.chr$chr.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \		runon -m 1024 vcfRefGen --in ALL.chr$chr.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \
	--out chr$chr.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz \		--out chr$chr.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz \
	--minAC 2 --filterList chr$chr.filter.regions		--minAC 2 --filterList chr$chr.filter.regions
	end		end
	</source>		</source>

2012-08-29T19:29:18Z

Example

← Older revision		Revision as of 15:29, 29 August 2012
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	runon -m 1024 vcfRefGen --in ALL.chr$chr.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \		runon -m 1024 vcfRefGen --in ALL.chr$chr.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz \
	--out chr$chr.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz \		--out chr$chr.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz \
	--minAC 2 --filterList chr$chr.filter.regions		--minAC 2 --filterList chr$chr.filter.regions
	end		end
	</source>		</source>