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, 22:40, 15 September 2014
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| After downloading the file, uncompress (unzip/untar) it. The directory created will be named <code>geneZoom</code>. | | After downloading the file, uncompress (unzip/untar) it. The directory created will be named <code>geneZoom</code>. |
| + | |
| + | == 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 |
| + | -------------------------------------- |