Protein Change Annotation from Oncotator

Question

[haiying.kong]

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?

Answer 1

[Vivek]

What file format are you supplying to oncotator? If its VCF, all the variants are assumed to be on the positive strand.

[haiying.kong]

Thank you for your reply. I think I was wrong. The software probably did right. But I am looking at BRAF one of the most studied genes. There are some strange protein changes, and if the strand is wrong, it can be explained. But as you said the strand is not wrong.

What could be the problem? the protein change is not right, and this gene has been so much studied, that I honestly do not believe I found any thing new.