Fig. 2
Use of replicates with primitive models. a Experimental steps in the typical NGS process. Errors can be generated at each step. Note that background errors in the library preparation step (red marks and bases) cannot be discriminated with the sequencing replicates (pseudo-replicates). b Description of primitive approaches (intersection and BAM-merge) with their expected (upper) and real (lower) effects. Each square represents an observed B allele for a given position. Positions with a number of B alleles beyond the detection threshold (red dashed line) are called as mutation candidates (positions with black squares). Both approaches are expected to discriminate true variants (orange-shaded positions) from false calls based on the randomness of error (upper). However, in real high-depth data, both approaches are ineffective due to excessive background errors (lower). c Sensitivity and FPR of the primitive approaches with sample B (1% VAF) for each platform. Primitive approaches were applied for both library (solid lines) and sequencing (dotted lines) duplicates. Calls from the single sample (dashed lines) are also depicted to evaluate the improvement with replicates. All mutation calls were made by MuTect. Source data are provided as a Source Data file
