Support for b38/hg38

[alexramos]

Not needed anytime soon but will be eventually needed sometime in 2015.

[alanhoyle]

We are hoping to transition to hg38 here as well, and Oncotator supporting the updated genome would be a boon to that move.

[alanhoyle]

Just wondering, what would be required to help to make this happen?

[alexramos]

Hi Alan, I no longer work on the Oncotator project. Your best best is to ping Lee Lichtenstein directly for this.

…

-Alex

On Fri, Feb 3, 2017 at 12:01 PM, Alan Hoyle ***@***.***> wrote: Just wondering, what would be required to help to make this happen? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#281 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACQWiWbRMbNbkOEtgrWwBIOKj60E41svks5rY4eJgaJpZM4DIjUN> .

[sooheelee]

FYI, I believe VEP is GRCh38 compatible.

[alanhoyle]

@LeeTL1220 any timeline for hg38 support? Or should we move to VEP or another solution (do you have a suggestion)?

[LeeTL1220]

hg38 support in Oncotator has been put off indefinitely. Apologies for any inconvenience. If that changes, I'll post here. I know a lot of people that like VEP.

…

On Thu, May 18, 2017 at 2:27 PM, Alan Hoyle ***@***.***> wrote: @LeeTL1220 <https://github.com/leetl1220> any timeline for hg38 support? Or should we move to VEP or another solution (do you have a suggestion)? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#281 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACDXk86LoHlu3-YFgsRhFKsQAiGspIqYks5r7I2vgaJpZM4DIjUN> .

-- Lee Lichtenstein Broad Institute 75 Ames Street, Room 7003EB Cambridge, MA 02142 617 714 8632

[jason-weirather]

Hi @LeeTL1220 Is the status of hg38 for Oncotator still put off indefinitely? I see there has not been a lot of commits so I'm guessing its not coming but wanted to double check. Thanks!

[LeeTL1220]

@jason-weirather It is not coming. I would direct you to see GATK4 Funcotator, which will be handling hg38 in much the same way as Oncotator. Funcotator is still in beta, but should be able to handle the most common Oncotator use cases soon.

https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_funcotator_Funcotator.php

More Funcotator docs are on the way. Feel free to post in the GATK4 forum with any questions or help requests.