Changes between Version 23 and Version 24 of SnpAnnotationPipeline


Ignore:
Timestamp:
Jan 5, 2011 11:04:55 AM (11 years ago)
Author:
a.kanterakis
Comment:

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  • SnpAnnotationPipeline

    v23 v24  
    506506 * To Annotate a VCF (version 4.0) file, use: http://www.bbmriwiki.nl/svn/SequenceAnnotation/Scripts/ANNOVAR.py This is a wrapper for the ANNOVAR tool.
    507507 * Usage:
     508 * 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    * --pathToANNOVAR: The path to the installed ANNOVAR tool
     510    * --VCFFilename: The path to the VCF file to be annotated
     511    * --outputFilename: The output annotated file
     512    * --outputDirectory: output directory
     513    * --buildver: Could be either hg18 or hg18
     514    * --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
     518    * --
    508519= Related work =
    509520