Two sets of designed benchmarks targeting low-frequency SNVs from both Ion Proton and Illumina MiSeq [15] sequencing technologies were included. The details of these 2 datasets are described in Methods section and Additional files 2 and 3. Briefly, the Ion Proton training benchmark is the sequencing data from a single individual with known genotypes, while the test benchmark was designed to mimic the paired normal-tumor design for somatic SNVs identification applications. The Illumina MiSeq benchmark data were generated by mixing 4 individuals at 4 different percentages and then permuted the mixing percentage assignment 4 times to generate 4 calibration datasets – CAL_A, CAL_B, CAL_C and CAL_D. Since the 4 calibration data sets were generated with the same procedures, without loss of generality, we used CAL_A as training benchmark and treated the others as testing benchmark.
