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  1. IGB
  2. IGBF-3748

Add individual genome CRAM file to IGB quickload via svn

        Details

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

          Description

          Situation: We have identified a publicly available Nebula Genomics CRAM file (link). Nowlan has downloaded the file and created an index, and was able to view the file in IGB. We would like to make this file available to IGB users as an example of a consumer genomics CRAM file.

          Task: Upload and deploy the CRAM file (NB72462M.cram), CRAM index, VCF file, and VCF index and make them available through an IGB Quickload. Also deploy the IGBF-3841 via the annots.xml.

          Note: Data are from Personal Genome Project
          Link to metadata in PGP: https://my.pgp-hms.org/profile/huF7A4DE
          Link to PGP search page: https://my.pgp-hms.org/public_genetic_data

          Revision:

          • Scope increase - include Nebula Genomics and Sequence.com data files for Donor 1
          • Scope increase - explore data in region of BRCA1 as preliminary use case, beginning tutorial

            Attachments

            1. annots.xml
              2 kB
            2. BothFiles-Donor1-BRCA1.png
              BothFiles-Donor1-BRCA1.png
              201 kB
            3. BRCA1-chr17-43092417.png
              BRCA1-chr17-43092417.png
              114 kB
            4. chrEBV_error.txt
              18 kB
            5. quickload_v3.zip
              9 kB
            6. rs80357336.png
              rs80357336.png
              181 kB

              Issue Links

              blocks

              Documentation - When documentation is missing or wrong IGBF-3988 Add CRAM tutorial to the User's Guide

              • Major - Major loss of function.
              • To-Do
              is blocked by

              Epic - Created by JIRA Software - do not edit or delete. Issue type for a big user story that needs to be broken down. IGBF-3871 Release IGB 10.1.0

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

              Task - A task that needs to be done. IGBF-3841 Deploy new NEBULA data for human genome sequencing / CRAM demo

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3846 Design and print a poster for ASHG 2024 (Paige's)

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-4063 Fix individual genome Quickload being displayed on the wrong genome

              • Major - Major loss of function.
              • To-Do

                Activity

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: