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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

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3642 [ IGBF-3642 ]
                nfreese Nowlan Freese made changes -
                Sprint Summer 1 [ 195 ]
                nfreese Nowlan Freese made changes -
                Sprint Summer 2 [ 196 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 [ 196 ] Summer 2, Summer 3 [ 196, 197 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Summer 2, Summer 3 [ 196, 197 ] Summer 2 [ 196 ]
                nfreese Nowlan Freese made changes -
                Sprint Summer 2 [ 196 ] Summer 2, Summer 4 [ 196, 198 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 4 [ 196, 198 ] Summer 2 [ 196 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                nfreese Nowlan Freese made changes -
                Sprint Summer 2 [ 196 ] Summer 2, Summer 6 [ 196, 200 ]
                nfreese Nowlan Freese made changes -
                Assignee Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3841 [ IGBF-3841 ]
                nfreese Nowlan Freese made changes -
                Attachment quickload.zip [ 18462 ]
                nfreese Nowlan Freese made changes -
                Description Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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.                 		Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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.

                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?utf8=%E2%9C%93&data_type=&commit=Search
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Summary Deploy Nebula Genomics CRAM file to web Add individual genome CRAM file to IGB quickload via svn
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 6 [ 196, 200 ] Summer 2, Summer 6, Summer 7 [ 196, 200, 201 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-3854 [ IGBF-3854 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Description Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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.

                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?utf8=%E2%9C%93&data_type=&commit=Search                 		Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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.

                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
                nfreese Nowlan Freese made changes -
                Epic Link IGBF-1765 [ 17855 ] IGBF-3856 [ 23155 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Attachment quickload_V2.zip [ 18473 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Link This issue is blocked by IGBF-3871 [ IGBF-3871 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Description Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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.

                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                 		Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 6, Summer 7 [ 196, 200, 201 ] Summer 2, Summer 6, Summer 7, Fall 1 [ 196, 200, 201, 202 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Attachment annots.xml [ 18485 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Attachment quickload_v3.zip [ 18486 ]
                nfreese Nowlan Freese made changes -
                Sprint Summer 2, Summer 6, Summer 7, Fall 1 [ 196, 200, 201, 202 ] Summer 2, Summer 6, Summer 7, Fall 2 [ 196, 200, 201, 203 ]
                nfreese Nowlan Freese made changes -
                Sprint Summer 2, Summer 6, Summer 7, Fall 2 [ 196, 200, 201, 203 ] Summer 2, Summer 6, Summer 7, Fall 3 [ 196, 200, 201, 204 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3846 [ IGBF-3846 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 6, Summer 7, Fall 3 [ 196, 200, 201, 204 ] Summer 2, Summer 6, Summer 7, Fall 3, Fall 4 [ 196, 200, 201, 204, 205 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 6, Summer 7, Fall 3, Fall 4 [ 196, 200, 201, 204, 205 ] Summer 2, Summer 6, Summer 7, Fall 3, Fall 4, Fall 5 [ 196, 200, 201, 204, 205, 206 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Summer 2, Summer 6, Summer 7, Fall 3, Fall 4, Fall 5 [ 196, 200, 201, 204, 205, 206 ] Summer 2, Summer 6, Summer 7, Fall 3, Fall 4, Fall 6 [ 196, 200, 201, 204, 205, 207 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 6, Summer 7, Fall 3, Fall 4, Fall 6 [ 196, 200, 201, 204, 205, 207 ] Summer 2, Summer 6, Summer 7, Fall 3, Fall 4, Fall 6, Fall 7 [ 196, 200, 201, 204, 205, 207, 208 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Link This issue blocks IGBF-3988 [ IGBF-3988 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 6, Summer 7, Fall 3, Fall 4, Fall 6, Fall 7 [ 196, 200, 201, 204, 205, 207, 208 ] Summer 2, Summer 6, Summer 7, Fall 3, Fall 4, Fall 6, Fall 7, Fall 8 [ 196, 200, 201, 204, 205, 207, 208, 209 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Description Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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                 		Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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
                ann.loraine Ann Loraine made changes -
                Description Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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                 		Situation: We have identified a publicly available Nebula Genomics CRAM file ([link|https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/]). 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
                ann.loraine Ann Loraine made changes -
                Attachment quickload.zip [ 18462 ]
                ann.loraine Ann Loraine made changes -
                Attachment quickload_V2.zip [ 18473 ]
                ann.loraine Ann Loraine made changes -
                Attachment rs80357336.png [ 18598 ]
                ann.loraine Ann Loraine made changes -
                Attachment chrEBV_error.txt [ 18599 ]
                ann.loraine Ann Loraine made changes -
                Attachment BothFiles-Donor1-BRCA1.png [ 18600 ]
                ann.loraine Ann Loraine made changes -
                Attachment BRCA1-chr17-43092417.png [ 18606 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                pkulzer Paige Kulzer made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                pkulzer Paige Kulzer made changes -
                Story Points 1 3
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-4063 [ IGBF-4063 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: