Fig. 1

Flowchart of the variant calling workflow. The variant calling workflow consists of two separate branches. A basic workflow already generates a set of usable, functionally annotated variants (SNPs and indels). A second, optional workflow, uses the previously called variants to perform Base Quality Score Recalibration (BQSR) to improve initial base calls of the fastq files. Processing of each individuals fastq files can be performed in parallel. Also various steps of the workflow can be parallelized, e.g. base calling on genomic intervals by the GATK HaplotypeCaller, as indicated by overlapping boxes. Each box includes a description of the step (light gray), the name of the used application (medium gray) and the primary input and output data formats (dark gray)