Fig. 2

Pairwise variant discordance rates were calculated between pipelines from each of five centers (pre-harmonization and post-harmonization) as well as between independent sequencing replicates of the same individuals processed by the same pipeline (data replicates). From left, single nucleotide (SNV) and small insertion/deletion (indel) variants were detected with GATK, and structural variants (SV) with LUMPY. The pre-harmonization and post-harmonization comparisons include 14 independently sequenced samples. The data replicate comparisons include four replicates of NA12878 and two replicates of NA19238. Note that the extremely high levels of discordance for SVs pre-harmonization are largely due to variable use of decoy sequences in the reference genomes used by the different centers. The center line is the median, the upper and lower hinges are the first and third quartiles, and the whiskers extend to the largest/smallest values no further than 1.5 * inter-quartile range from the hinge