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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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Processing VCF files by vcf2maf with OncoKB™ isoforms? #212

Closed Teezi closed 9 months ago

Teezi commented 9 months ago

Hi,

I'm new to the oncokb-annotator and I'm a bit confused by the sentence in your README file that says "We recommend processing VCF files by vcf2maf with OncoKB™ isoforms." Could you please clarify what this means? I've already used vcf2maf (umccr version) to convert my VCF file to MAF format. Do I need to add any additional arguments when running vcf2maf?

Any guidance would be greatly appreciated!

zhx828 commented 9 months ago

Hi,

I'm new to the oncokb-annotator and I'm a bit confused by the sentence in your README file that says "We recommend processing VCF files by vcf2maf with OncoKB™ isoforms." Could you please clarify what this means? I've already used vcf2maf (umccr version) to convert my VCF file to MAF format. Do I need to add any additional arguments when running vcf2maf?

Any guidance would be greatly appreciated!

I don't think so. The language is meant to remind you that please pay attention to your transcript whether it matches with ours when annotating on protein level. The genomic level annotation will pick OncoKB transcript automatically. That said, I agree with you the language is misleading. I removed the OncoKB isoform language.

Teezi commented 9 months ago

Ah, I understand now! Thank you so much for explaining it to me.