Feature Request: Show all tracks OR show all VARIANT tracks

[sdanzige]

The IGV web interface is unbelievably useful. However, sometimes I run into a problem where there's only a few variants and a lot of wild-type fragments. When this happens, IGV will downsample and I can only see 1-2 out of 10 variant fragments. I understand that there's an option in the desktop version to show all tracks, but I haven't been able to find it in the web interface.

Really, I don't want to see all tracks, I want to see all variant tracks. However, either option would solve my problem.

Thank you,
-S

[jrobinso]

Sorry for the delayed response. Correct me if I'm wrong, but I think what you are requesting is to see all alignments, or see only "variant" alignments, in an alignment track (bam or cram). This is not possible, and would potentially be difficult. At a minimum we would have to define a "variant" alignment. Even then, I'm not sure it will be possible to do this in real time. But a definition would be a start.

[sdanzige]

I apologize I was not clear.
By 'variant', I mean a nucleic acid fragment with a mutation in it. For example, a SNP. I'm generally looking tumor cells, which have both wild-type and variant fragments that map to the same location.

What I would like is to see all of the fragments, and especially those fragments with mutations in them. Using the IGV web interface, if there's a lot of fragments then downsampling occurs. If I sort the fragments by the nucleic acid at a specific location, then the fragments with the mutation usually come to the top. However, because of the downsampling, I often see fewer mutated fragments than I expect.

The option I would like is:

1. To turn off downsampling OR
2. Only see fragments with mutations in them; I don't need to see the wildtype fragments.

[jrobinso]

Got it, I think, I'm still making the assumption that we are talking about an alignment track.

We can do (1). It might cause your browser to freeze in particularly deep coverage areas.

[sdanzige]

Thank you! Hopefully if it crashes, it will just take down the tab.