PACBIO alignment on IGV

Question

[jan]

Hi All,

I have some candidate strucutral variants (sequenced from Pacbio platform) that need to be inspected on IGV. For most of them, it's pretty obvious to tell but for some, especially insertions, I'm not too sure how to make of it.

Based on the short guide on Pacbio, the insertion labels were aligned on most reads.

However, for some of my insertions, the labels were scattered accross the reads, and I'm not too sure if they are real or artefacts? What are the crieteria to look for when assessing alignment from Pacbio platform (alligned and called using Pacbio specific pipeline, pbmm2 and pbsv).

Below are some examples of candidate insertions where their labels are scattered accross the reads.

Answer 1

[Istvan Albert]

In these situations the quick consensus mode is misleading, it makes it appear that the only differences are in the large insertions.

Turn off the "quick consensus" option (righ click) and investigate the matches.

It is likely that the reads have a good number of different errors that produce misleading alignments. In this case as long as the insertions are the same I would consider the most likely point to be the insertion and the shifts are artifacts of the alignments.