Enhancing breakpoint resolution with deep segmentation model: a general refinement method for read-depth based structural variant callers

MotivationFor short-read sequencing, read-depth based structural variant (SV) callers are difficult to find single-nucleotide-resolution breakpoints due to the bin-size limitation. ResultsIn this paper, we present RDBKE to enhance the breakpoint resolution of read-depth SV callers using deep segmentation model UNet. We show that UNet can be trained with a small amount of data and applied for breakpoint enhancement both in-sample and cross-sample. On both simulation and real data, RDBKE significantly increases the number of SVs with more precise breakpoints. Availabilitysource code of RDBKE is available at https://github.com/yaozhong/deepIntraSV Contactyaozhong@ims.u-tokyo.ac.jp