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  1. IGB
  2. IGBF-1791

Investigate new file format for personal genome visualization

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: Various personal genomics providers (23andMe and Ancestry) provide raw data in slightly different formats. The current IGB app transforms this data into the BED format, which is viewable by IGB. However, this is not optimal as BED format has many unused fields that are filled with default values.

          Task: Investigate what would be the optimal data format for 23andMe or Ancestry data. Most likely we will need to create a new format.

            Attachments

              Issue Links

              relates to

              Epic - Created by JIRA Software - do not edit or delete. Issue type for a big user story that needs to be broken down. IGBF-2246 Create new App to show results from personal genotyping platforms

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1788 [ 17878 ]
                nfreese Nowlan Freese made changes -
                Link This issue blocks IGBF-1792 [ IGBF-1792 ]
                nfreese Nowlan Freese made changes -
                Priority Blocker [ 1 ] Major [ 3 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Take a look at the VCF file format . May be useful if we do not need to include all of the columns.

                Show
                nfreese Nowlan Freese added a comment - Take a look at the VCF file format . May be useful if we do not need to include all of the columns.
                aloraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18513 ] Fall 2019 Workflow Update [ 18981 ]
                aloraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 18981 ] Revised Fall 2019 Workflow Update [ 21101 ]
                Status Open [ 1 ] In Progress [ 3 ]
                aloraine Ann Loraine made changes -
                Summary Investigate new file format Investigate new file format for personal genome visualization
                aloraine Ann Loraine made changes -
                Epic Link IGBF-1788 [ 17878 ] IGBF-1908 [ 17998 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ]
                aloraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                aloraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                aloraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                aloraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                aloraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                aloraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                aloraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                aloraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                aloraine Ann Loraine made changes -
                Link This issue relates to IGBF-2246 [ IGBF-2246 ]
                Hide
                Permalink
                aloraine Ann Loraine added a comment -

                Removing attachments to reduce space required on jira host.

                Downloaded to my local in case we need to save them.

                Show
                aloraine Ann Loraine added a comment - Removing attachments to reduce space required on jira host. Downloaded to my local in case we need to save them.
                aloraine Ann Loraine made changes -
                Attachment ancestry.txt.zip [ 14328 ]
                aloraine Ann Loraine made changes -
                Attachment genome_Nowlan_Freese_Full_20140925065254.zip [ 14327 ]

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: