Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:4
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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.
Attachments
Issue Links
- relates to
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IGBF-1291 Show soft-clipped bases in BAM files
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Labels | Advanced |
| Rank | Ranked higher |
| Assignee | Ivory Blakley [ ieclabau ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| 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. Steve's contact info will be sent via email (for privacy). |
| Status | In Progress [ 3 ] | Reviewing [ 10301 ] |
| Assignee | Ivory Blakley [ ieclabau ] | Ann Loraine [ aloraine ] |
| Fix Version/s | 9.0.1 Minor Release [ 10500 ] |
| Fix Version/s | 9.0.1 Minor Release [ 10500 ] |
| Sprint | B - Summer 2018 [ 48 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | B - Summer 2018 [ 48 ] |
| Rank | Ranked lower |
| Rank | Ranked lower |
| Sprint | B - Summer 2018 [ 48 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018 [ 48 ] |
| Rank | Ranked lower |
| 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. Steve's contact info will be sent via email (for privacy). |
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. |
| Summary | Ensure IGB shows soft-clipped bases from read alignments correctly | Check if IGB shows soft-clipped bases from read alignments correctly |
| Resolution | Done [ 10000 ] | |
| Status | Reviewing [ 10301 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 17904 ] | Fall 2019 Workflow Update [ 19844 ] |
| Workflow | Fall 2019 Workflow Update [ 19844 ] | Revised Fall 2019 Workflow Update [ 21963 ] |