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10 bytes removed
, 22:41, 15 September 2014
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| Note: | | Note: |
− | The SNPs and VCF should be hg19 version.
| + | The SNPs and VCF should be hg19 version. |
− | VCF file must have the header greater than 4.0 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).
| + | 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 |
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| ------------------------------------- | | ------------------------------------- |
| 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 --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
| + | 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 |
| -------------------------------------- | | -------------------------------------- |