I ran oncotator on MuTect2 output. I found that the strand is not taken in consideration when protein change is decided.
For instance, if the SNV is G>A on negative strand, on positive strand it should be C>T, and when we decide the protein change, we should consider C>T, bot G>A. But the oncotator software seem to treat every thing on positive strand. Is there any easy way to fix this?