Fig. 1

Highlights of functional equivalence standard. We defined a series of required and allowed processing steps that provide flexibility in pipeline implementation while keeping variation between pipelines at a minimum. Reads must be aligned to a specific reference genome using a minimum version of the BWA-MEM aligner. Algorithms for marking duplicates and recalibrating base quality scores are more flexible and vary somewhat between centers. Compression of quality scores into four bins saves storage and file transfer costs, while maintaining acceptable accuracy and sensitivity