Input somatic mutations are not actually somatic?

[chaos66ren]

Dear Professor Chen,

In investigating the application of this software to the WES dataset, I found that some somatic mutations derived from Varscan2 (using the Varscan2 default command: java -jar VarScan.v2.3.9.jar somatic XXX.mpileup YYY.mpileup) seem not somatic actually. Would such a phenomenon affect the optimization of purity estimate because this step takes the somatic mutations into consideration? And, more importantly, would it affect the quantification of intratumor heterogeneity (this procedure compares the distribution of somatic mutation and the germline mutation distribution)? If the somatic mutations are wrongly adopted, the final results of heterogeneity evaluation might be biased.

I am looking forward to hearing from you.

Best wishes,