Enhancing breakpoint resolution with deep segmentation model: a general refinement method for read-depth based structural variant callers
Zhang, Y.-z.; Imoto, S.; Miyano, S.; Yamaguchi, R.
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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
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