Comparison of variant base frequency in the SNVs and corresponding positions in the matching normal samples. (A) Common. (B) MuTect only. (C) SomaticSniper only. Each single dot corresponds to the variant base frequency in the tumor and normal samples for: (A) SNVs identified in AMLs by both pipelines (SomaticSniper and MuTect) and corresponding positions in the normal samples (“common”; B-C), and SNVs identified exclusively by MuTect or SomaticSniper and corresponding positions in the normal samples (“MuTect only”; “SomaticSniper only”). Black dots correspond to validated SNVs, gray dots with black circle to not-validated SNVs, and gray dots are not tested SNVs. We noticed that the majority of not-validated SNVs in MuTect appear at very low frequencies. Two not-validated SNVs in SomaticSniper hit known driver genes of AML (TET2 and DNMT3A); we think that the presence of these variants in the normal sample can be due to the contamination with tumor DNA given by the minimal residual disease.