Tablet not showing pileup indels

[agc]

Hi,

I have a pileup file with the following line:

chr4	103518793	*	*/+TA	20	20	33	6	*	+TA	5	1	0	0	0

I understand this implies that there is an indel at position 103518793 on chr4. However, upon opening the bam file in tablet and checking said location, I see 6 reads, none of which support an indel.

Does anyone know what might cause this?

Thanks.

[gaffa]

Tablet does not display insertions by putting a gap in the reference sequence, but by putting an annotation in a feature track running alongside the alignment. This is the "CIGAR-I" track (if you don't have it by default you should be able to add it in "Select Tracks" in the "Features" tab) - an insertion is marked by a big "I" in this track, hoover the "I" and it shows you what read(s) have the insertion.

It works but it's a bit awkward in my opinion. Having an option for displaying gaps in the reference sequence (like in e.g. samtools tview) would be pretty neat.