Figure 1: Analytical pipeline flow diagram. A, broad overview of operations highlighting the interactions between the wet-laboratory and scientists with the analytical pipeline; B, all inputs, outputs, and programs used at each step in the analytical pipeline. A, aligned; S, sorted; PCRM, PCR duplicates marked; PCRR, PCR duplicates removed; I, indexed; IR, indels realigned; RR, random read-sampled.