Change default transcript of IGV in Patient View

[jjgao]

We noticed that TP53 x125_splice fell out of the refseq annotation of TP53, e.g in this patient.

Digging more, it looks like that the transcript used by IGV can be different from the ones used by cBioPortal and it seems like we are only showing the first two refseq IDs in the patient view (but missing the scrollbar to show more as in igv web)

Questions:

• Is it possible to display the scroll bar too?
• Ideally we set the transcript as the same as what's used in cBioPortal.

[jrobinso]

Are you defining your own reference object for the cBio portal? The default annotation for igv.js, "Refseq All", has many more than 2 transcripts for TP53. What annotation file are you using for cBio?

[jrobinso]

RE the scrollbar, if you don't see the scrollbar there is nothing to scroll (you are seeing everything).