-r parameter ignored?

[vaipathak]

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]

@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.