I have been using VarScan and MuTect to call somatic variants. Lately, of curiosity, I also tried to call variants separately for the tumor sample (vs hg19) and normal sample (also vs hg19) using GATK, and compared the outputs, which is - I thought - theoretically also the somatic variants. However, the number of variants found this way is way more than the one found by VarScan or MuTect.
My questions is: What's wrong with doing so? Is that because some systematic errors in the algorithm somehow got doubled when calling variants separately?
Thank you very much.