I'm working on rather standard whole-exome sequencing data and treat it the same as whole-genome sequencing data (aligning it to the full GRCh38 reference assembly and calling variants with no exome-related parameters).
I recently noticed that my variant calling results contain numerous variants mapped to a non-exomic region, incidentally, some of them were significantly associated with the phenotype I study.
My questions are as follows:
- Are the non-exome variants in my exome data invalid? or could it be that the exome kit captured more than it was designed to capture?
- Should I treat raw exome sequencing data any different than genome sequencing data, and if so, what parts of my pipeline should be modified to accommodate exome data?