Gnomad4 annotator failing due to missing Tabix

[Clare86]

Describe the bug
gnomad4 annotator is failing to run.

To Reproduce
Use the GUI interface to annotate a vcf file
Select Gnomad4 and click Annotate.

Logs show
Error initializing gnomad4: No module named 'tabix'
Error running gnomad4: cannot access local variable 'annotator' where it is not associated with a value

Desktop (please complete the following information):

• OS: Mac
• Browser: Chrome
• Open Cravat Version 2.17

Additional context
I've run pip install pytabix and I have tried reinstalling Open Cravat, gnomad4 and Python. Nothing has worked.
It was working when using OC version 2.13.

[hip-hopanonymous]

Same problem here using the windows installer on windows 11. Everything else seems to be working fine, just gnomad4 is having this issue

Edit: I see from #359 that this isn't supported in Windows, so a separate issue for me.

[RachelKarchin]

Hi Clare86,

Thanks for your feedback.

We offered an older, smaller version of the Gnomad annotator in the past. This is what worked for you on Windows previously. It was not related to the version of OpenCRAVAT.

Gnomad4 has grown much larger than previous versions and tabix is the best solution we've found for very large annotators that are too big for our standard sqlite format.

Tabix is not supported on Windows machines. We are not aware of any alternatives to Tabix for Windows at this time.

[Clare86]

Hi Rachel.

Thanks for the response. Just to note though, hip-hopanonymous said they were on Windows but I'm on a Mac. I do have tabix installed.

[Clare86]

I decided to check the previous versions of Open Cravat. Gnomad4 runs in 2.13, 2.15 and 2.16. I did get a division by 0 error in the log, but I could handle that with some edits to the python script.

Clearly the tabix issue is specific to 2.17.