Hi!

I have an annotated vcf file generated by mutect2 and flagged by FliterMutectCalls.

Thing is, I have found my variant of interest but it is not flagged as PASS but as "orientation".

I want to know if the read orientation bias that has been detected in this variant would be enough to discard it or instead it is still acceptable as valid.

I have seen that some variant calling platforms like Varsome eg do accept the orientation bias as a PASS variant (https://docs.varsome.com/en/variant-calling-and-quality-filters).

It is the first time I perform an analysis of this kind, and would love to know what is the best way to interpret this result.

Thanks !!