Figure 1

Resolution improvement by exploiting concordant read pairs. Schematic illustration of the key idea of our method ChopSticks. Unlike conventional SV detection methods based only on discordant pairs whose mapping distances were not close to the expectation, ChopSticks uses concordant read pairs as well. There is a chance that there is a concordant read closer to the boundary of the deleted region (breakpoint) than any discordant reads. Such a concordant read localizes the predicted position of the breakpoint, and therefore it contributes to achieving a high resolution. In this figure, b is the upstream end of a true deletion, Δ _b is the distance between the upstream end of a true deletion and that of a deletion call by threshold-based read-pair (RP) methods. Similarly, ${\Delta }_b^{\prime }$ is defined for our method. The expected values of Δ _b and ${\Delta }_b^{\prime }$ are given by Equations (2) and (3), respectively.