Changes between Version 24 and Version 25 of SnpAnnotationPipeline


Ignore:
Timestamp:
Jan 5, 2011 11:58:54 AM (11 years ago)
Author:
a.kanterakis
Comment:

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  • SnpAnnotationPipeline

    v24 v25  
    507507 * Usage:
    508508 * Example: python ANNOVAR.py --pathToANNOVAR /data/home/akanterakis/tools/ANNOVAR/annovar  --VCFFilename /data/home/data/pdeelen/Celiac40ExomsProject/SequenceData/sequence0605_41.index_hg18.snps.filtered.vcf --outputFilename /data/home/data/alex/ANNOVAR/annotated/output.txt --outputDirectory /data/home/data/alex/ANNOVAR/annotated/ --buildver hg18 --annotationDirectory /data/home/data/alex/ANNOVAR/humandb_hg18/ --geneBasedAnnotations refgene,knowngene,ensgene --regionBasedAnnotations band,segdup,dgv,gwascatalog --filterBasedAnnotations snp130 --customAnnotations kantale
     509 * Options:
    509510    * --pathToANNOVAR: The path to the installed ANNOVAR tool
    510511    * --VCFFilename: The path to the VCF file to be annotated
     
    513514    * --buildver: Could be either hg18 or hg18
    514515    * --annotationDirectory: The directory where the annotation files are
    515     * --geneBasedAnnotations: Gene Based Annotations according to ANNOVAR
    516     * --regionBasedAnnotations: Region Based Annotations according to ANNOVAR
    517     * --filterBasedAnnotations: Filter Based Annotations according to ANNOVAR
     516    * --geneBasedAnnotations: Gene Based Annotations according to ANNOVAR (coma separated no spaces)
     517    * --regionBasedAnnotations: Region Based Annotations according to ANNOVAR (coma separated no spaces)
     518    * --filterBasedAnnotations: Filter Based Annotations according to ANNOVAR (coma separated no spaces)
     519    * --customAnnotations: Custom annotations. These should be GFF3 files http://www.sequenceontology.org/gff3.shtml. The list of files should be comma separated no spaces
     520    * --dummy: If set True, the script will not do anything just print the script commands. Default value: False
    518521    * --
    519522= Related work =