Difference between revisions of "Genezoom"
Line 56: | Line 56: | ||
Note: | Note: | ||
− | + | The SNPs and VCF should be hg19 version. | |
− | + | VCF file must have the header greater than 4.0 version. | |
− | + | This tool will run ANOVAR to annotate VCF. The annotation values should be in the value list of ANOVAR(http://www.openbioinformatics.org/annovar/annovar_gene.html). | |
Version : 1.0.1 | Version : 1.0.1 | ||
Line 65: | Line 65: | ||
------------------------------------- | ------------------------------------- | ||
Usage : | Usage : | ||
− | + | perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --flag "splicing:0.01:0.02,nonsense:blue,missense" --format pdf --outDIR outDIR | |
− | + | perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --snpChrFieldName chr --snpPosFieldName pos --snpDelim tab/comma/blank --flag "splicing:green,nonsense:0.02:0.03,missense" --lables "chr1:123,chr2:234" --outDIR outDIR | |
-------------------------------------- | -------------------------------------- |
Revision as of 22:41, 15 September 2014
GeneZoom plot is a visualization tool that shows the frequency of variants in a predefined region for groups of individuals. It takes an annotated VCF file as input and generate a text file with specific variant information extracted from VCF file. An R script is used to draw GeneZoom plot based on the text file.
Because all reference data are version hg19, please make sure that your VCF file is also version hg19.
Get geneZoom Source Codes
Download from webpage
Through this link geneZoom Download, you can download a copy of geneZoom.
Download from GitHub with Git
You can create your own git clone(copy) using:
git clone https://github.com/jinchen-umich/geneZoom.git
or
git clone git://github.com/jinchen-umich/geneZoom.git
Either of these two commands creates a directory called geneZoom in the current directory.
Update your copy
If you have already downloaded your copy, use the following commands to update:
1. cd pathToYourCopy/geneZoom 2. git pull
Download From GitHub without Git
If there is no git in your system, you can still download from GitHub:
- Latest Code (master branch)
- via Website
- Go to : https://github.com/jinchen-umich/geneZoom
- Click on the
Download ZIP
button on the right side panel.
- via Command Line
- via Website
After downloading the file, uncompress (unzip/untar) it. The directory created will be named geneZoom
.
Build geneZoom
To build geneZoom, copy the geneZoom package to the directory you want, and then run the following command:
tar xzvf geneZoom.tar.gz
After you unzip, you can find 3 directories in "geneZoom" (./example ./lib ./scripts ./ref).
Basic Usage Example
When you run
perl geneZoom.pl
you will get some information about geneZoom
GeneZoom.pl :
This tool is a visualization tool that shows the frequency of variants in a predefined region for groups of individuals.
Note: The SNPs and VCF should be hg19 version. VCF file must have the header greater than 4.0 version. This tool will run ANOVAR to annotate VCF. The annotation values should be in the value list of ANOVAR(http://www.openbioinformatics.org/annovar/annovar_gene.html).
Version : 1.0.1
Report Bug(s) : jich[at]umich[dot]edu
Usage : perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --flag "splicing:0.01:0.02,nonsense:blue,missense" --format pdf --outDIR outDIR
perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --snpChrFieldName chr --snpPosFieldName pos --snpDelim tab/comma/blank --flag "splicing:green,nonsense:0.02:0.03,missense" --lables "chr1:123,chr2:234" --outDIR outDIR