Update genecode mapper

[cheanney]

Hi,

We are attempting to annotate all variants for the KRT86 gene. Based on the HG38 genomic location of KRT86, we obtained all gnomAD v4 variants within this region. While exploring the OpenCRAVAT results, we discovered that all variants were assigned to AC021066.1 instead of KRT86. The Ensembl transcript ID is ENST00000293525.5. We verified this transcript on Ensembl, and it is indeed assigned to KRT86. We then checked the Gencode version used in the mapper, which is version 33. The latest version is 44. We are wondering if the Gencode mapper in OpenCRAVAT can be updated.

Here is one of the variants we investigated:

chr12 52306237 G A Yes AC021066.1 ENST00000293525.5

Thanks

[RachelKarchin]

Sorry for our slow response. This is a hugely important issue and we will be prioritizing it. Stay tuned for updates.

[cheanney]

Just want to check about this issue. GeneCode version is now 47. OpenCravat is still using version 33.

[skanderson]

We are in the final testing phases of upgrading our mapper to GeneCode 46. We are aiming to release the update next week.

[cheanney]

greatly appreciated!!

[cheanney]

Any news on GeneCode 46?

[kmoad]

Hi @cheanney

We have an updated mapper with gencode 47 that's out now on run.opencravat.org.

It does assign your variant to KRT86

Could you check it out and let us know if it's getting the transcripts you expect?

[cheanney]

@kmoad Thanks for the update. I checked online and confirmed that the expected transcript is now available. What’s the timeline for pushing the GENCODE update to the OpenCRAVAT command line?

[kmoad]

Gencode 47 mapper should be available to all oc users now. You can install it from the GUI by going to the update section of the store, or by running oc module update.

[cheanney]

Sorry to bother you again, but I don't see gencode v47. It is still v33. When I did oc module update, I don't see gencode as an annotator to update.

[kmoad]

Hmm. You should see the hg38 module updating to version 1.47.0. It would look like this

kyle@monolith:~$ oc module update
Name  New Version  Size      
hg38  1.47.0       732.0 MB  
Update the above modules? (y/n) > 

It may be that your install of opencravat isn't high enough though. There were some changes a couple years ago that require opencravat to be at least version 2.4.0. These changes weren't related to the gencode update, but it would still restrict installing the newest hg38. You can check this with oc version.