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
- Closed
If we want to change the way that soft-clipped bases are shown, we could try to direct IGB to process the CIGAR string as if that 'S' (soft-clipped) were 'X' (mis-match). IGB determines what is a match or a mismatch based on the sequence itself. So the real key would be to make IGB use the whole sequence including the soft-clipped bases. This might require adjusting the sequence length attribute and the alignment start position attribute. ...and potentially more that I haven't thought of yet.