<p>Hello,</p>

<p>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.</p>

<p>My questions is: What&#39;s wrong with doing so? Is that because some systematic errors in the algorithm somehow got doubled when calling variants separately?</p>

<p>Thank you very much.</p>

There are posts that hint at a lot of this if you do a search on here. The short answer is that somatic mutation calling is a different beast. To give just one example, single sample (germline) calling, you can assume that the frequency of SNPs will generally be 50% or 100%. In tumors, you have to take purity, ploidy, and tumor heterogeneity into account and SNPs may occur across a wide range of VAFs.

We get into all of this a little bit in our recent paper here: [Optimizing Cancer Genome Sequencing and Analysis](http://www.cell.com/cell-systems/abstract/S2405-4712(15)00113-1)