Mercury Data Flow. 1) Sequencing Instrument raw data is passed to vendor primary analysis software to generate sequence reads and base call confidence values (qualities). 2) Reads and qualities are passed to a mapping tool (BWA) for comparison to a reference genome to determine the placement of reads on the reference (producing a BAM file). 3) Individual sequence event BAMs are merged to make a single sample-level BAM file that then is processed in preparation for variant calling. 4) Atlas-SNP and Atlas-indel are used to identify variants and produce variant files (VCF). 5) Annotation adds biological and functional information to the variant lists and formats them for delivery.