I am trying to find subclonal variants in a sample sequenced with high coverage (a ~1000x gene panel). After using mutect2 to call SNVs and INDELs in normal-matched mode, I've detected that some of the called variants also exist in its normal-matched.
For example: the VAF of a called variant in the tumour is 0.1 (supported by 18 reads out of 1787), but its VAF in the matched-normal is 0.02 (supported by 5 reads out of 864).
Why do you think the variant is called? Shouldn't it be considered germline?
Please sign in to leave a comment.