Changes between Version 6 and Version 7 of SnpAnnotationPipeline


Ignore:
Timestamp:
Nov 24, 2010 12:43:37 PM (12 years ago)
Author:
a.kanterakis
Comment:

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  • SnpAnnotationPipeline

    v6 v7  
    77 * xercesImpl-2.6.1.jar
    88
     9== Parameters ==
     10For a complete list of parameters please check the [http://gvs.gs.washington.edu/SeattleSeqAnnotation/|SeattleSeq Annotation website] and the example below
     11
     12== Example ==
     13{{{
     14#!div style="font-size: 80%"
     15Code highlighting:
     16  {{{#!python
     17AnnotateVarianListFileViaSeattleSeqAnnotation(
     18        inputFile=/Users/alexandroskanterakis/Data/SNP/chr1.snp.Q20.gff,
     19        outputFile=/Users/alexandroskanterakis/Tools/annotation/seattleseqannotation/output.txt,
     20        eMail=alexandros.kanterakis@gmail.com,
     21        fileFormat=GFF,
     22        geneData=CCDS2008,
     23        allelesMaq=true,
     24        allelesDBSNP=true,
     25        scorePhastCons=true,
     26        scorePhastCons=true,
     27        consScoreGERP=true,
     28        chimpAllele=true,
     29        CNV=true,
     30        geneList=true,
     31        HapMapFreqType=HapMapFreqMinor,
     32        geneList=true,
     33        hasGenotypes=true,
     34        dbSNPValidation=true,
     35        repeats=true,
     36        geneList=true,
     37        proteinSequence=true,
     38        polyPhen=true,
     39        clinicalAssociation=true
     40        )
     41  }}}
     42}}}
     43
     44== Source Code ==
     45http://www.bbmriwiki.nl/svn/SequenceAnnotation/SubmitSeattleSeqAnnotationAutoJob/SubmitSeattleSeqAnnotationAutoJob.py
    946= Pipeline Elements =
    1047