Incorrect view for duplications on reverse strand

[mihailefter]

Incorrect view for duplications on reverse strand

[mihailefter]

@jfjlaros Maybe using a different approach for a duplication variant, similar to a repeat/delins would be better?

[jfjlaros]

Why do we need any visualisation apart from that of a delins?

[mihailefter]

This is what we currently do. An ins is visualized as a delins with no deleted part and a dup is also visualized as an ins (as in the first image above), but it could be also visualized as in the bottom picture.

[jfjlaros]

I would not make any exceptions for different types of variants. I also do not think this is the problem here.

The description NC_000023.11(NM_000109.4):c.8-3dup is just syntactic sugar for NC_000023.11(NM_000109.4):c.8-3_8-2insT, which should be visualised just like NC_000023.11(NM_000109.4):c.8-3_8-2insG.

[mihailefter]

The ins view was also my initial choice, but now, considering that a dup is actually a repeat where the repeat number is 2, I think that it should also be visualized as such, similar to NC_000023.11(NM_000109.4):c.8-3T[2]. Of course, for this example the normalized description should be maybe NC_000023.11(NM_000109.4):c.8-6_8-3T[5], but this is a different discussion.

[jfjlaros]

I would just fix this issue in the most straightforward way possible. We can discuss more complicated visualisation approaches at a later stage.