Cigar string doesn't match IGV read visualization

[tanyasarkjain]

Hi,
I am viewing some aligned reads on IGV as well as programmatically examining the cigar strings in my region of interest. I noticed not all the insertions/deletions present as indicated by the cigar are visible on the reads in IGV. I validated these insertions/deletions do exist using BAMview. Wondering if there is a setting to view all insertions/deletions in all reads? Not sure if some are getting filtered out.

[jrobinso]

What version of IGV are you using? There is an option to hide small indels, enabled by default for long reads. This is controlled by user preference (View > Preferences). See the user documentation for more details.

[tanyasarkjain]

I am using 2.17.3, which setting is it? I have tried adjusting the coverage allele frequency

[jrobinso]

The setting is "Hide Indels < show indel threshold"