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  1. IGB
  2. IGBF-543

Improve Selection Info present for VCF file Insertions

        Details

        • Type: Improvement
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:

          Description

          It seems that VCF files are supported by IGB but the insertions in the VCF file have no Selection Info, even though there is much relevant information within the tooltips for these insertions.

          This should be fixed in the near future.

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              mason Mason Meyer (Inactive) created issue -
              mason Mason Meyer (Inactive) made changes -
              Field Original Value New Value
              Epic Link IGBF-497 [ 15559 ]
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              ann.loraine Ann Loraine made changes -
              Story Points 0.5
              mason Mason Meyer (Inactive) made changes -
              Attachment TooltipInfoDoesntMatchSelectionInfo.png [ 13950 ]
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              ieclabau Ivory Blakley (Inactive) added a comment -

              Comment from issue IGBF-1380
              ___________________________

              The changes for 4.2 (compared to 4.1)

              • INFO field can have one value for each possible allele (code R).
                This allows one more possible special value to the number value for an INFO field. IGB does not currently read/use this field. No change needed.
              • For all of the ##INFO, ##FORMAT, ##FILTER, and ##ALT meta information, extra fields can be included after the default fields.
                As part of a general improvement to the parser, we should include a map for each entry that would be able to these open form values. These values would be part of the selection info for an entry, but they will not affect how the entry is displayed. This can be handled as part of issue IGBF-543.
              • Alternate base (ALT) can include *: missing due to a upstream deletion.
                I am still figuring out if/how the code might need to change to accommodate this. None of my example v4.2 files use this option.
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              ieclabau Ivory Blakley (Inactive) added a comment - Comment from issue IGBF-1380 ___________________________ The changes for 4.2 (compared to 4.1) INFO field can have one value for each possible allele (code R). This allows one more possible special value to the number value for an INFO field. IGB does not currently read/use this field. No change needed. For all of the ##INFO, ##FORMAT, ##FILTER, and ##ALT meta information, extra fields can be included after the default fields. As part of a general improvement to the parser, we should include a map for each entry that would be able to these open form values. These values would be part of the selection info for an entry, but they will not affect how the entry is displayed. This can be handled as part of issue IGBF-543 . Alternate base (ALT) can include *: missing due to a upstream deletion. I am still figuring out if/how the code might need to change to accommodate this. None of my example v4.2 files use this option.
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              ieclabau Ivory Blakley (Inactive) added a comment - - edited

              The <*> notation is explained in section 5.5 of the VCF format specification, but I am still unclear about how this type should be represented. I don't know if the END tag is mandatory when the <*> is used. I think using the END tag when it is present should be part of our general improvement to the parser.

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              ieclabau Ivory Blakley (Inactive) added a comment - - edited The <*> notation is explained in section 5.5 of the VCF format specification, but I am still unclear about how this type should be represented. I don't know if the END tag is mandatory when the <*> is used. I think using the END tag when it is present should be part of our general improvement to the parser.
              ann.loraine Ann Loraine made changes -
              Epic Link IGBF-497 [ 15559 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Summary There is no Selection Info present for VCF file Insertions Improve Selection Info present for VCF file Insertions
              ieclabau Ivory Blakley (Inactive) made changes -
              Assignee Ivory Blakley [ ieclabau ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status Open [ 1 ] Open [ 1 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Sprint Fall 2018 Sprint 2 [ 52 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Rank Ranked lower
              ieclabau Ivory Blakley (Inactive) made changes -
              Status Open [ 1 ] In Progress [ 3 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status In Progress [ 3 ] Open [ 1 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status Open [ 1 ] In Progress [ 3 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status In Progress [ 3 ] Open [ 1 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status Open [ 1 ] In Progress [ 3 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Status In Progress [ 3 ] Open [ 1 ]
              ann.loraine Ann Loraine made changes -
              Sprint Fall 2018 Sprint 2 [ 52 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Assignee Ivory Blakley [ ieclabau ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 15813 ] Fall 2019 Workflow Update [ 18759 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 18759 ] Revised Fall 2019 Workflow Update [ 20881 ]
              Status Open [ 1 ] To-Do [ 10305 ]
              ann.loraine Ann Loraine made changes -
              Epic Link IGBF-1765 [ 17855 ]
              ann.loraine Ann Loraine made changes -
              Labels Intermediate

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                • Assignee:
                  Unassigned
                  Reporter:
                  mason Mason Meyer (Inactive)
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                  Dates

                  • Created:
                    Updated: