Variant Calling Algorithms Benchmark Using High Performance Computing

The application of Next Generation Sequencing to Whole GenomeSequencing is still showing enhanced advantages in many research fields suchas medical diagnostics. Here we conducted a comparative assessment ofGATK3-HaplotypeCaller, FreeBayes and Samtools-mpileup, three state ofthe art variant calling algorithms, on a "gold standard" benchmark. Theanalyses were performed exploiting the high performance computing technologyof ReCaS datacenter. Our results indicated that Samtools-mpileup was themost conservative with the highest precision, followed by FreeBayes andGATK3-HaplotypeCaller, which presented the highest sensitivity. Moreover,the merged call-set resulted in lower sensitivity and precision, suggestingadditional testing using different merging methods followed by wet-labvalidations. Despite some limitations, these results provide important insightsfor the development and refinement of novel bioinformatics tools and workflows.