igvteam/igv.js

Represent filter

Closed this issue · 2 comments

Andy-B-123 commented

Hi, thank you for your work on this! I'm looking to use igv-reports to highlight certain variants of interest from a background set of variants.

I use the "FILTER" column in the VCF for this and in the desktop version of IGV the variants are greyed out as shown:
image

However with igv-report the filter information doesn't seem to be visually displayed (although it is still there if manually inspecting the variant):
image

Would there be a way of having the FILTER column be able to be used to adjust opacity/colour? Or should I look to have that information as part of the INFO column? If so, any quick advice for colouring things by the INFO column?

Thank you!

jrobinso commented

This would be an issue for igv.js, I'm transferring the issue to that project.

  • 👍1
jrobinso commented

This is implemented in igv.js, post release we will update igv-reports. If you want to test it beforehand edit your report and change the igv.js script import near the top of the page to this

<script src="https://igv.org/web/snapshot/dist/igv.min.js"></script>