A computer implemented method of identifying a structural genomic rearrangements in massively parallel nucleic acid sequencing data, comprising: (a) obtaining massively parallel sequencing information for one or more genomic regions as nucleic acid sequence reads; (b) aligning said nucleic acid sequencing reads to one or more reference sequences; (c) selecting nucleic acid sequencing reads which only partially map to said reference sequence, wherein a portion of the nucleic acid sequencing reads remains unmapped, constituting a soft-clipped region, wherein the soft-clipped nucleotides of the nucleic sequencing read is at least 8 to 15 nucleotides long; (d) creating groups of nucleic acid sequencing reads as selected in step (c), all of which are defined by identical start or end positions of said soft-clipped regions; (e) generating a synthetic consensus sequence for each group as obtained in step (d), wherein said consensus sequence is based on the abundance of identical nucleotides at a position; Characterized in that it further comprises: (f) identification of pairs of synthetic consensus sequences as candidates for structural genomic rearrangements by generating combinations of positions between (i) groups of nucleic acid sequencing reads, wherein soft-clipped nucleotides are at the start of the nucleic acid sequence, and (ii) groups of nucleic acid sequencing reads, wherein said soft-clipped nucleotides are at the end of the nucleic acid sequence, by comparing the synthetic consensus sequence of step (e) with the reference sequence; (g) pairing nucleic acid sequencing reads which match at respective positions in the reference sequence; and (h) detecting a structural genomic rearrangement if both synthetic consensus sequences of pairs as obtained in step (g) match at respective positions in the reference sequence. (a) obtaining massively parallel sequencing information for one or more genomic regions as nucleic acid sequence reads; (b) aligning said nucleic acid sequencing reads to one or more reference sequences; (c) selecting nucleic acid sequencing reads which only partially map to said reference sequence, wherein a portion of the nucleic acid sequencing reads remains unmapped, constituting a soft-clipped region, wherein the soft-clipped nucleotides of the nucleic sequencing read is at least 8 to 15 nucleotides long; (d) creating groups of nucleic acid sequencing reads as selected in step (c), all of which are defined by identical start or end positions of said soft-clipped regions; (e) generating a synthetic consensus sequence for each group as obtained in step (d), wherein said consensus sequence is based on the abundance of identical nucleotides at a position; (f) identification of pairs of synthetic consensus sequences as candidates for structural genomic rearrangements by generating combinations of positions between (i) groups of nucleic acid sequencing reads, wherein soft-clipped nucleotides are at the start of the nucleic acid sequence, and (ii) groups of nucleic acid sequencing reads, wherein said soft-clipped nucleotides are at the end of the nucleic acid sequence, by comparing the synthetic consensus sequence of step (e) with the reference sequence; (g) pairing nucleic acid sequencing reads which match at respective positions in the reference sequence; and (h) detecting a structural genomic rearrangement if both synthetic consensus sequences of pairs as obtained in step (g) match at respective positions in the reference sequence. <EOS>