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oncokb / oncokb-annotator

Annotates variants in MAF with OncoKB annotation.
GNU Affero General Public License v3.0
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Logical to filter VCFs to OncoKB gene list before annotation? #211

Closed SpikyClip closed 9 months ago

SpikyClip commented 9 months ago

I process large VCFs and am looking to annotate them using OncoKB MafAnnotator.py in an efficient way. I was wondering if its appropriate to filter VCFs to the OncoKB gene list with BCFtools (taking advantage of multithreading speed) then annotating the output with OncoKB.

The main question is whether the gene list above is completely inclusive of all possible annotations produced by MafAnnotator.py? The second question is whether this might be redundant if OncoKB is already doing this under the hood.

zhx828 commented 9 months ago

@SpikyClip sorry about the late reply. No need to filter, OncoKB already doing that.

SpikyClip commented 9 months ago

Ended up pre-filtering (because I had a pre-filtering step anyway with other rules) keeping all variants that intersected with a bed file containing all the genes in the oncokb gene list. I don't think(?) I am missing any possible annotations this way.

zhx828 commented 9 months ago

Ended up pre-filtering (because I had a pre-filtering step anyway with other rules) keeping all variants that intersected with a bed file containing all the genes in the oncokb gene list. I don't think(?) I am missing any possible annotations this way.

Sure, but make sure for fusion event, check both genes.