IGV not highlighting possible variants

Question

[francois]

Surely this is trivial, but I have looked everywhere and I cannot find the answer...

IGV sometimes does not want to highlight the possible variants in the coverage track (i.e. when it does the boxplot of the different allele frequencies).

The problem does not come from the Set allele frequency threshold option. I have tried changing it to 0.1, and it still does not do it.

Can you help?

Here is an example of when it should highlight the variant, but does not do it: https://ibb.co/jt5CEo

[WouterDeCoster]

I don't see the reference genome sequence here either.

[francois]

Ah, you are right! I did not notice it, but obviously that is linked to the problem. Any idea what is happening? I loaded hg38 directly from IGV...

[Kairos]

May you have active the "quick consensus mode"? That and the allele frequency threshold are the only options that come to my mind.

[francois]

Did not seem to be the problem, but good to know, thank you.

[francois]

I closed IGV, re-opened it and re-loaded hg38 and now it works. Who knows what went wrong... Thanks a lot!

Answer 1

[francois]

Thanks @WouterDeCoster.

Just so we can close the post:

I closed IGV, re-opened it and re-loaded hg38 from the Menu in the top left.

Seems to work now!