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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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-r parameter ignored? #186

Open vaipathak opened 1 year ago

vaipathak commented 1 year ago

Hi, I'm using the latest version of OncoKb-annotator with MafAnnotator. When I include the -r parameter with the command to use GRCh38 as the reference, it seems to be ignored and it runs GRCh37 instead. I'm running the following:

python3.9 MafAnnotator.py -i Chr1.maf -o Chr1_annot.maf -r GRCh38 -b Onco-KB Token

Thanks!

zhx828 commented 1 year ago

@vaipathak I do have a test covering reference genome. Could you send me a slice of your data to reproduce? Is it possible your data row also has reference genome info and it will overwrite the default through command line.