Breakpoint interval size distributions for structural variation calls in NA12878. LUMPY refines the location of a given breakpoint by taking the product of the probability distributions in the breakpoint’s evidence set. The shape of each distribution depends on the breakpoint uncertainty that is inherent to the evidence signal type (for example, the spatial uncertainty of breakpoints predicted by paired-end alignments is much higher than with split-read alignments). (A) The distribution of predicted breakpoint intervals for SV calls when using solely paired-end alignments. The variability in fragment size causes a significant amount of uncertainty in the paired-end signal, which results in a wide (over 500 bases for the NA12878 sample) distribution in the predicted breakpoint intervals. (B) The distribution of predicted breakpoint intervals for SV calls when using solely split-read alignments. Split-read alignments inherently have far less uncertainty in the predicted breakpoint location and, therefore, they yield a distribution with much lower variance. (C) The resulting breakpoint uncertainty distribution when both paired-end and split-read alignments are jointly considered. By taking the product of the distributions, the inherent breakpoint precision afforded by split-read alignments is not substantially diluted by paired-end alignments. (D) A comparison of the predicted breakpoint intervals reported by GASVPro (left) all LUMPY calls (center), and the 95% confidence interval for the LUMPY calls (right). Size distributions are not shown for DELLY or Pindel since they only report single base coordinates. stdev, standard deviation.