Deletions occasionally not showing since IGV 2.5+ versions

[R...@lbl.gov]

We use IGV to display alignments and error calls of Pacbio sequencing of various plasmid constructs.

Most of the people in my group are still using IGV 2.4.x. Rarely with particular constructs IGV versions since the 2.4.x series aren't displaying single-base deletions in the ROI reads. Most of the time deletions are displayed properly.

IGV 2.4.14 (Mac) showing the deletion:

IGV 2.5.3 not showing the deletion (replicated in IGV 2.7.0):

[R...@lbl.gov]

After installing 2.7.0 I looked at 3 or 4 other alignments with single-base deletions in 2.7.0 and am seeing the same behavior, whereas 2.5.3 is showing the deletions correctly, including now for some reason in the example above.

[James Robinson]

A number of features were added specifically for pacbio with the 2.5 release, one of those was to hide small indels by default.  The threshold is 2 bases.   You can change it in preferences (View > Preferences...), see screenshot.    You can read about it here:  https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/

To see these indels just uncheck the box in preferences

On Thu, Oct 17, 2019 at 2:04 PM <R...@lbl.gov> wrote:

After installing 2.7.0 I looked at 3 or 4 other alignments with single-base deletions in 2.7.0 and am seeing the same behavior, whereas 2.5.3 is showing the deletions correctly, including now for some reason in the example above.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/41e7ba5e-1bd9-4b37-af31-ce3dc1b44fcb%40googlegroups.com.

[R...@lbl.gov]

Thanks very much James, that fixes it.