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Workflow Wizard

The wizard has 3 4 pages.

  1. Input Variations: On this page, you must input variations file(s).  

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    <center>
      <br>
      <img src="/wiki/download/attachments/16122730/Variation Annotation with SnpEff_1.png"/>
      <br> 
    </center>
  2. Change chromosome notation for variations: On this page you can change the chromosome notation for variations.  

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    <center>
      <br>
      <img src="/wiki/download/attachments/16122730/Variation Annotation with SnpEff_2.png"/>
      <br> 
    </center>

    The following parameters are available:

    Replace prefixesInput the list of chromosome prefixes that you would like to replace. For example "NC_000". Separate different prefixes by semicolons.
    Replace byInput the prefix that should be set instead, for example "chr".
  3. SnpEff Parameters: On this page you can modify SnpEff parameters.  
    HTML
    <center>
      <br>
      <img src="/wiki/download/attachments/16122730/Variation Annotation with SnpEff_3.png"/>
      <br> 
    </center>

    The following parameters are available:

    GenomeSelect the target genome. Genome data will be downloaded if it is not found.
    Cannonical transcriptsUse only cannonical transcripts
    HGVS nomenclatureAnnotate using HGVS nomenclature

    Annotate Loss of function

    Annotate Loss of function (LOF) and Nonsense mediated decay (NMD)


    Annotate TFBSs motifsAnnotate transcription factor binding site motifs (only available for latest GRCh37)
    Upstream/downstream lengthUpstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length
  4. Output: On this page, you need input output parameters.  
    HTML
    <center>
      <br>
      <img src="/wiki/download/attachments/65930434/Variation Annotation with SnpEff_4.png"/>
      <br> 
    </center>