The application of next-generation sequencing in clinical routine requires valid variant calling results. However, the evaluation of several open-source tools has pointed out that variant calling remains challenging.

We present appreci8, an automatic pipeline for calling single nucleotide variants and short indels by combining and filtering the output of eight open-source variant calling tools, based on an artifact- and a polymorphism score. To train appreci8, we analyzed two data sets from patients with myelodysplastic syndrome, covering 165 Illumina samples. Appreci8's performance was tested by analyzing five independent data sets, covering 513 samples. Variation in sequencing platform, target region and disease entity was considered. All calls were validated by re-sequencing on the same platform, a different platform or expert-based review.

Sensitivity of appreci8 ranged between 0.93 and 1.00, while positive predictive value ranged between 0.65 and 1.00. In all cases, this performance is comparable or better than the best individual tool.