Hi,
I see that the CLIN_SIG column - ClinVar annotation - was removed when moving from genie v.5 to v6.
Could you please share why it is no longer available?
We would like to use v11 because it contains many more patients, but we need the pathogenicity annotation.
Is such data available?
Thank you!
Michal
Created by mich Thanks! Hello,
We rely on [Genome Nexus annotation pipeline](https://github.com/genome-nexus/genome-nexus-annotation-pipeline) tool to re-annotate variants and create the final MAF for release. Incorporating additional columns would require an update to this tool. If there are specific columns you are interested in, I would recommend adding your input to the following [issue](https://github.com/genome-nexus/genome-nexus-annotation-pipeline/issues/68) to prioritize use cases for the update and specifying exactly which columns that you would be most interested in seeing added.
Best,
Haley Hi again :)
Another option would be to retain only some of the annotations - the top priority ones - and get rid of the rest. Hi Haley,
Thank you for your reply, and for making this valuable data available!
I'd like to continue the discussion started there.
I think a typical use-case of this data would require the missing annotation, which gives indications about the significance of the variants.
I do realize the annotated file gets really big when containing 120K samples... but I wander if there's a different way to solve the problem.
Perhaps to supply two different versions of mutation file - one with the annotation and another without it?
I think most users would need the annotation, but it's not trivial to get it once the VCF is turned to MAF.
VEP doesn't accept MAF as input, so it would take some work to produce a VEP-input file from the MAF you created.
Some of the users would not know how to do it, and in any case it's time consuming and error-prone, and at the end - one still ends up downloading the huge file!
I wander what do you and other users think about it.
Michal Hi Maayan!
[Release 5.0](https://www.synapse.org/#!Synapse:syn17112456.1) has the ClinVar annotation, but this release only has ~35K samples, compared to ~120K samples in the current release (v11).
Hi @mich ,
Please see the explanation posted on a previous thread: https://www.synapse.org/#!Synapse:syn7222066/discussion/threadId=5683
Best,
Haley Hello Michal,
I can't reply to your question (I'm a user of the GENIE datasets as well) but was wondering which file are you looking at that has the ClinVar annotation?
Maayan.