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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
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GeneZoom.pl :
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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
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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
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