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LocusZoom Standalone (view source)

Revision as of 14:28, 31 May 2017

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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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=== Fine-mapping credible sets ===
 
=== Fine-mapping credible sets ===
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LocusZoom can add an additional track to the plot showing results from a fine-mapping analysis. These are typically SNPs within the 95% credible set (see [http://www.nature.com/ng/journal/v44/n12/full/ng.2435.html this paper] for an example.)
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LocusZoom can add an additional track to the plot showing results from a fine-mapping analysis. These are typically SNPs within the 95% credible set (see [http://www.nature.com/ng/journal/v44/n12/full/ng.2435.html this paper] for an example of a method generating such a set of SNPs.)
    
To add this fine-mapping track, you supply (as a plotting option) the fine-mapping set of credible SNPs as a file:  
 
To add this fine-mapping track, you supply (as a plotting option) the fine-mapping set of credible SNPs as a file:  
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[[File:New lz finemap summary.png|400px]]
 
[[File:New lz finemap summary.png|400px]]
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=== Labeling multiple SNPs ===
 
=== Labeling multiple SNPs ===
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</pre>
 
</pre>
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The BED file should have 4 columns: the first 3 for chr/start/end, and the 4th column for the label of the track.
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The BED file should have at least 4 columns: the first 3 for chr/start/end, and the 4th column for the label of the track. It must be '''tab-delimited''', not white-space delimited.
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Color can also be specified, but the BED file then needs to follow the full [http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED format].
    
=== Specify gene table (refFlat, GENCODE, etc.) ===
 
=== Specify gene table (refFlat, GENCODE, etc.) ===
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|-
 
|-
 
| colorCol=NULL
 
| colorCol=NULL
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| Specify the name of a column in association results file denoting the color each marker should be. This disables coloring by LD.  
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| Specify the name of a column in association results file denoting the color each marker should be. This disables coloring by LD. For the column values, color names should be used, for example "red" "olivedrab" etc.  
 
|-
 
|-
 
| signifLine=NULL
 
| signifLine=NULL
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| Specify (in p-value scale) where to place a horizontal significance line. Can have multiple lines, e.g. signifLine="5e-08,1e-10"
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| Specify (in -log10 p-value scale) where to place a horizontal significance line. Can have multiple lines, e.g. signifLine="7.3,9"
 
|-
 
|-
 
| signifLineColor=NULL
 
| signifLineColor=NULL
Welchr
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