LocusZoom Standalone 1.2 - Revision history

Goncalo: Redirected page to LocusZoom Standalone

2014-12-03T18:46:32Z

← Older revision		Revision as of 14:46, 3 December 2014
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	[[LocusZoom_Standalone~~\|See LocusZoom Standalone~~]]		#REDIRECT [[LocusZoom_Standalone]]

2013-05-09T20:31:10Z

← Older revision		Revision as of 16:31, 9 May 2013
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	[[LocusZoom_Standalone]]		[[LocusZoom_Standalone\|See LocusZoom Standalone]]

2013-05-09T20:30:55Z

2013-05-09T20:30:41Z

Blanked the page

2013-05-09T18:37:30Z

GWAS catalog variants

← Older revision		Revision as of 14:37, 9 May 2013
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	=== GWAS catalog variants ===		=== GWAS catalog variants ===

	You can add known GWAS variants to your plots ~~with the following~~:		You can add known GWAS variants to your plots. For example:

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">

2013-05-09T18:37:14Z

GWAS catalog variants

← Older revision		Revision as of 14:37, 9 May 2013
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	~~lzdev~~ --gwas-cat whole_cat-significant-only --build hg19 ~~...~~		locuszoom ... --gwas-cat whole_cat-significant-only --build hg19
	</syntaxhighlight>		</syntaxhighlight>

2013-05-09T18:36:54Z

GWAS catalog variants

2013-05-09T18:36:41Z

Plotting LD with additional reference SNPs

← Older revision		Revision as of 14:36, 9 May 2013
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	Will generate the following plot:		Will generate the following plot:

	[[File:New lz cond only.png\|~~900px~~]]		[[File:New lz cond only.png\|700px]]


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	\| Bins for LD		\| Bins for LD
	\|}		\|}


	=== GWAS catalog variants ===		=== GWAS catalog variants ===

2013-05-09T18:36:08Z

Supply VCF files for calculating LD

← Older revision		Revision as of 14:36, 9 May 2013
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	This option takes the place of having to supply per-region pre-calculated LD (--ld) or having to specify --pop and --source for calculating LD from genotype files supplied by LZ.		This option takes the place of having to supply per-region pre-calculated LD (--ld) or having to specify --pop and --source for calculating LD from genotype files supplied by LZ.

	<span style="color:#FF6600">'''Warning: '''</span> The VCF file must also have a tabix index located in the same directory. For the above example, the tabix index "my_genotypes.vcf.gz.tbi" must exist.		<span style="color:#FF6600">'''Warning: '''</span> The VCF file must also have a [http://samtools.sourceforge.net/tabix.shtml tabix] index located in the same directory. For the above example, the tabix index "my_genotypes.vcf.gz.tbi" must exist.

2013-05-09T18:30:07Z

← Older revision		Revision as of 14:30, 9 May 2013
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	* [[#Fine-mapping credible sets\|Fine-mapping credible sets]]		* [[#Fine-mapping credible sets\|Fine-mapping credible sets]]
	* [[#GWAS catalog variants\|GWAS catalog variants]]		* [[#GWAS catalog variants\|GWAS catalog variants]]
			* [[#Supply VCF files for calculating LD\|Supply VCF files for calculating LD]]

← Older revision		Revision as of 14:30, 9 May 2013
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	* [[#Fine-mapping credible sets\|Fine-mapping credible sets]]		* [[#Fine-mapping credible sets\|Fine-mapping credible sets]]
	* [[#GWAS catalog variants\|GWAS catalog variants]]		* [[#GWAS catalog variants\|GWAS catalog variants]]
			* [[#Supply VCF files for calculating LD\|Supply VCF files for calculating LD]]