Figure 4.

Agreement across pipelines with and without recommended parameters. A+B+C+D) Agreement across pipelines without recommended parameters. E+F+G+H) Agreement across pipelines with recommended parameters. A+E) Agreement on Illumina SNP calls. B+F) Agreement on Illumina InDel calls. C+G) Agreement on Oxford Nanopore (ONT) SNP calls. D+H) Agreement on ONT InDel Calls. For each figure, the bars indicate the number of variants called by the groups indicated by filled circles below, across the whole dataset. The large number of workflow unique calls for LANL and BEI in C) and D) respectively are attributable to calls with low read support (DP<100 or ALTDP<50), of low frequency (<50%), in homopolymer regions, or in samples with poor reference coverage, as indicated by the reduction after filtering, G) and H) respectively.