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  1. IGB
  2. IGBF-4082

Investigate: How is IGB 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 IGB is parsing and displaying a VCF file. This will include naming key classes in IGB 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

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              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-4083 Investigate: How is IGV parsing and displaying VCF files?

              • Major - Major loss of function.
              • Closed

                Activity

                  People

                  • Assignee:
                    sjagarap saideepthi jagarapu (Inactive)
                    Reporter:
                    pkulzer Paige Kulzer (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: