Fig. 1.

Analysis workflow. Schematic representation of the workflow of analyses applied to the NA12878 platinum genome dilution series. Raw data have been initially analysed using two alignment pipelines (BWA/GATK-based and Novocraft-based) with or without base quality recalibration. Somatic calls were identified using two distinct tools: Mutect2 and Strelka. For base quality recalibrated data, mutation caller parameters have been adjusted to improve overall performance. The intersection between mutations from the same caller but different alignment pipelines was selected to reduce the number of false positives. Subsequently, the unions of these filtered calls from Mutect2 and Strelka were combined to obtain the final set of calls