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  1. IGB
  2. IGBF-3907

Investigate adding additional Samtools tags to Filter/Color By options in IGB

        Details

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

          Description

          Situation: Samtools specifies several tags for SAM/BAM files which provide additional information. Karthik has added CR and CB tags to the Filter/Color By option in IGB as part of IGBF-3881.

          Task: Investigate which additional Samtool tags may be worth adding to the Filter/Color By option in IGB. While it may be easy to add many/all tags, consider if they would be useful to the end user and how that might affect the user interface.

          Note that there may be custom tags specific to certain tools.

          Samtools tags documentation: https://samtools.github.io/hts-specs/SAMtags.pdf
          Cell Ranger Samtools tag documentation: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-bam

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3880 Investigate samtools tags consistency across datasets from Cell Ranger

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3881 Add samtools filter by and color by options for CR and CB tags

              • Major - Major loss of function.
              • Closed

                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-3765 [ 22984 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3880 [ IGBF-3880 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3881 [ IGBF-3881 ]
                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 -
                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 -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Karthik Raveendran [ karthik ]

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: