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LocusZoom Standalone (view source)

Revision as of 13:00, 16 May 2018

1,338 bytes removed ,  13:00, 16 May 2018
→‎METAL formatted file
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For the latest stable LocusZoom package, see our [https://statgen.sph.umich.edu/locuszoom/download/ download] page. The current version is '''1.3''', released on June 20th, 2014.   
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For the latest stable LocusZoom package, see our [https://github.com/statgen/locuszoom-standalone download] page. The current version is '''1.3''', released on June 20th, 2014.   
    
Currently only '''Unix/Linux''' is supported, though Mac OS X should be supported in a future release. Support for Windows may come at a much later date.
 
Currently only '''Unix/Linux''' is supported, though Mac OS X should be supported in a future release. Support for Windows may come at a much later date.
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== Download ==  
 
== Download ==  
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See our [https://statgen.sph.umich.edu/locuszoom/download/ download] page for links to the latest as well as previous releases.
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See our [https://github.com/statgen/locuszoom-standalone download] page for links to the latest as well as previous releases.
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== Changes in Version 1.3 ==
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New features:
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* Database and GWAS catalog files updated for hg19
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* [[#Plotting BED tracks| Adding BED tracks]]
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* [[#Updating the existing locuszoom database(s)| Update locuszoom's database without waiting for a release]]
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* [[#Specify gene table (refFlat, GENCODE, etc.) | Use different gene information tables + GENCODE support]]
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* [[#EPACTS formatted file|Support for tabix indexed EPACTS files]]
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* [[#Reading from STDIN| Read data from STDIN]]
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* [[#Plotting options| New plotting options for color, significance lines]]
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* [[#Supply VCF files for calculating LD|Provide multiple chromosome separated VCF files for calculating LD]]
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The full changelog is available on the [https://statgen.sph.umich.edu/locuszoom/download/ download] site.
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== Changes in Version 1.2 ==
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A number of new features have been added for this version. See the following sections for more info:
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* [[#EPACTS formatted file|Loading EPACTS results]]
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* [[#Plotting LD with additional reference SNPs|Plotting LD with additional reference SNPs]]
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* [[#Labeling multiple SNPs|Labeling multiple SNPs]]
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* [[#Fine-mapping credible sets|Fine-mapping credible sets]]
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* [[#GWAS catalog variants|GWAS catalog variants]]
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* [[#Supply VCF files for calculating LD|Supply VCF files for calculating LD]]
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The full changelog is available on the [https://statgen.sph.umich.edu/locuszoom/download/ download] site.
      
== Installation  ==
 
== Installation  ==
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| align="center" | 1.23e-04
 
| align="center" | 1.23e-04
 
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|-
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| align="center" | rs3
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| align="center" | chr4:401141
 
| align="center" | 9.4e-390
 
| align="center" | 9.4e-390
 
|}
 
|}
    
<br>  
 
<br>  
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Markers can be either rsIDs or chr:pos format (see above).
    
This file should be passed to locuszoom using the <code>--metal</code> option.  
 
This file should be passed to locuszoom using the <code>--metal</code> option.  
Welchr
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