Flowchart for analysis pipeline. A metadata file describing the sequence data being uploaded for analysis together with the location of the files are passed as input to a shell script. The shell script configures the VM on Amazons AWS and uploads data to the VM. A Galaxy workflow is used for Phase 1 of the analysis. QC results are examined to verify data meets quality thresholds. A second Galaxy workflow is used for Phase 2 of the analyses producing a VCF file containing variants.