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  1. IGB
  2. IGBF-4083

Investigate: How is IGV parsing and displaying VCF files?

        Details

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

          Description

          Task: Write a high-level overview of how IGV is parsing and displaying a VCF file. This will include naming key classes in IGV that are important for parsing and viewing the VCF file, as well as the overall flow.

          There are two types of VCF files we want to look at for this task: one with population-level information ("ALL.apol1.sample.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf" from the igvData.zip file) and one with individual-specific information ("NG1LRQNESI.hard-filtered.vcf.gz"). These files can be found on Google Drive in the VCF project folder: https://drive.google.com/drive/folders/1PTa3rcCp59BRUcd2mB8BfemK2d3Kn3n5?usp=drive_link

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-4106 Integrate htsjdk library for parsing VCF in IGB

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-4082 Investigate: How is IGB parsing and displaying VCF files?

              • Major - Major loss of function.
              • Closed

                Activity

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                pkulzer Paige Kulzer (Inactive) created issue -
                pkulzer Paige Kulzer (Inactive) made changes -
                Field Original Value New Value
                Epic Link IGBF-3836 [ 23135 ]
                pkulzer Paige Kulzer (Inactive) made changes -
                Link This issue relates to IGBF-4082 [ IGBF-4082 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 1 [ 210 ] Spring 1, Spring 2 [ 210, 211 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Assignee saideepthi jagarapu [ sjagarap ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Assignee saideepthi jagarapu [ sjagarap ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Link This issue is blocked by IGBF-4106 [ IGBF-4106 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                sjagarap saideepthi jagarapu (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    sjagarap saideepthi jagarapu (Inactive)
                    Reporter:
                    pkulzer Paige Kulzer (Inactive)
                  • Votes:
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                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: