Fig. 1

Circle-Map read realignment strategy. a Reads are mapped to the reference genome and discordantly aligned reads (green) and alignments containing soft clips (blue) are extracted; concordantly aligned reads (grey) are ignored. b Using the extracted reads, a graph of putative breakpoint connections between genomic regions is constructed and used as a prior to narrow down the genomic search space for realigning soft clipped reads. c Non-aligned parts of the soft clipped reads are realigned probabilistically using the breakpoint graph as guide. d Evidence from split-reads and discordant reads are combined to create the final circle calls together with information about concordant, split-read and discordant read coverage for each circle