Schematic illustration of the cuteSV approach. cuteSV uses sorted BAM file as input to detect SVs in 3 major steps. In step 1 (“discovering SV signatures”), cuteSV collects various types of SV signatures comprehensively from inter- and intra-alignments. In step 2 (“clustering of SV signatures”), a heuristic clustering-and-refinement method is employed to sensitively discover accurate SV alleles. In step3 (“SV calling and genotyping”), cuteSV generates the SV callsets and assigns genotypes
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