Diverse mechanisms of somatic structural variations in human cancer genomes

contains a mechanisms pipeline, similar to breakseq

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704973/#!po=42.5926

Cell. Author manuscript; available in PMC May 9, 2014.
Cell. May 9, 2013; 153(4): 919–929.
doi: 10.1016/j.cell.2013.04.010
PMCID: PMC3704973
NIHMSID: NIHMS475485

Diverse mechanisms of somatic structural variations in human cancer genomes Lixing Yang,1 Lovelace J. Luquette,1 Nils Gehlenborg,1,2 Ruibin Xi,1 Psalm S. Haseley,1,3 Chih-Heng Hsieh,4Chengsheng Zhang,4 Xiaojia Ren,3 Alexei Protopopov,5 Lynda Chin,5 Raju Kucherlapati,3,6 Charles Lee,4 and Peter J. Park1,3,7,*

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