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  1. IGB
  2. IGBF-1222

Check if IGB shows soft-clipped bases from read alignments correctly

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          4
        • Sprint:
          B - Summer 2018

          Description

          SAM specification allows for read alignments to be represented where the ends are "soft-clipped", meaning: they are not reported in the alignment.

          An IGB user noticed that older versions of IGB omitted these bases from the view. Instead, they should be shown, with mis-matches. This may have been fixed, but we need to check.

          If IGB shows the soft-clipped bases, users can more easily detect re-arrangements and other issues critical to diagnosing genomic defects in clinical samples.

          To start, make sure the above description of "soft-clipping" is correct.

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              Issue Links

              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1291 Show soft-clipped bases in BAM files

              • Major - Major loss of function.
              • Closed

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                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: