Changes between Version 16 and Version 17 of SnpAnnotationPipeline


Ignore:
Timestamp:
Nov 24, 2010 3:06:09 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • SnpAnnotationPipeline

    v16 v17  
     1= Introduction =
     2
     3{{{#!graphviz
     4
     5digraph g {
     6        size="10,10"
     7        node [shape=box,style=filled,color=white]
     8        "GFF Files from BGI"
     9        "Prepared GFF FIles files for SeattleSeq Annotation"
     10        "SeattleSeq Annotationed Files"
     11        "Polyphen Annotation"
     12        "GO From BioMart"
     13        "GO Annotation"
     14        "Intersection (Chr) Files"
     15        "VCF Files from 1000GP"
     16        "Allele Frequency Annotation"
     17        "Annotated Intersection Files"
     18
     19        node [shape=ellipse,color=yellow]
     20        PrepareGFFFilesFromBGIForSeattleSeqAnnotation
     21        AnnotateVarianListFileViaSeattleSeqAnnotation
     22        AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs
     23        AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl
     24        "AnnotationTool (Patrick)"
     25        CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames
     26        MergeHorizontallyFilesAccordingToCommonColumns
     27
     28        "GFF Files from BGI" -> PrepareGFFFilesFromBGIForSeattleSeqAnnotation -> "Prepared GFF FIles files for SeattleSeq Annotation" -> AnnotateVarianListFileViaSeattleSeqAnnotation -> "SeattleSeq Annotationed Files"
     29        "SeattleSeq Annotationed Files" -> AddPolyphenAnnotationToSNPsFromSeattleSeqAnnotationOutputs -> "Polyphen Annotation"
     30        "GO From BioMart" -> AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl
     31        "GFF Files from BGI" -> "AnnotationTool (Patrick)" -> "Intersection (Chr) Files"
     32        "Intersection (Chr) Files" -> AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl
     33        AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl -> "GO Annotation"
     34        "VCF Files from 1000GP" -> CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames
     35        "Intersection (Chr) Files" -> CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames
     36        CreateAlleleFrequencyAnnotationFilesForTabularFilenamesFromVCFFilenames -> "Allele Frequency Annotation"
     37        "Polyphen Annotation" -> MergeHorizontallyFilesAccordingToCommonColumns
     38        "GO Annotation" -> MergeHorizontallyFilesAccordingToCommonColumns
     39        "Allele Frequency Annotation" -> MergeHorizontallyFilesAccordingToCommonColumns
     40        "Intersection (Chr) Files" -> MergeHorizontallyFilesAccordingToCommonColumns
     41        MergeHorizontallyFilesAccordingToCommonColumns -> "Annotated Intersection Files"
     42        }
     43}}}
     44
     45
    146= PrepareGFFFilesFromBGIForSeattleSeqAnnotation =
    247Preprocesses GFF files coming from the BGI institute for SeattleAnnotationTool. Replace `alleles` with `allele` and adds the line: `# autoFile testAuto.txt` in the top of the file.