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  1. Jalview
  2. JAL-2835

Support visualisation of VEP (variant effect predictor) data

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.0
    • Component/s: None
    • Labels:
      None

      Description

      Extend 'load VCF' capability to also give drill down into the sub-fields of VEP data if present in the VCF file.
      For example, gnomAD VCF data set comes with VEP data - delimited sub-fields of the VCF field identified as CSQ.
      We want to be able to do analyse by these sub-fields in the same way as we can by the top level VCF fields, in particular:
      - filter on field values e.g. CSQ.PolyPhen Contains "damaging"
      - colour by field values e.g. CSQ.SIFT

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          Issue Links

          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-2069 Colour features by attribute value

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-2808 Filter features by attribute value conditions

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-2879 Save a map-valued feature attribute in Jalview project

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2792 Provide tabular view of (one) sequence feature's details

          • Major - Major loss of function.
          • Closed

          Story - Created by Jira Software - do not edit or delete. Issue type for a user story. JAL-2744 User controls to view and/or analyse by feature attributes

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. JAL-2843 Provide persistence for filter or colour by feature attribute

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated:
                Resolved: