BEDTools: a flexible suite of utilities for comparing genomic features. - Aaron R. Quinlan; Ira M. Hall (Bioinform., 2010)

YAHA: fast and flexible long-read alignment with optimal breakpoint detection. - Gregory G. Faust; Ira M. Hall (Bioinform., 2012)

Binary Interval Search: a scalable algorithm for counting interval intersections. - Ryan M. Layer; Kevin Skadron; Gabriel Robins; Ira M. Hall; Aaron R. Quinlan (Bioinform., 2013)

SAMBLASTER: fast duplicate marking and structural variant read extraction. - Gregory G. Faust; Ira M. Hall (Bioinform., 2014)

Population-based structural variation discovery with Hydra-Multi. - Michael R. Lindberg; Ira M. Hall; Aaron R. Quinlan (Bioinform., 2015)

SVScore: an impact prediction tool for structural variation. - Liron Ganel; Haley J. Abel; FinMetSeq Consortium; Ira M. Hall (Bioinform., 2017)

The impact of rare variation on gene expression across tissues. - Xin Li 130; Yungil Kim; Emily K. Tsang; Joe R. Davis; Farhan N. Damani; Colby Chiang; Gaelen T. Hess; Zachary Zappala; Benjamin J. Strober; Alexandra J. Scott; Amy Li; Andrea Ganna; et al. (Nat., 2017)

svtools: population-scale analysis of structural variation. - David E. Larson; Haley J. Abel; Colby Chiang; Abhijit Badve; Indraniel Das; James M. Eldred; Ryan M. Layer; Ira M. Hall (Bioinform., 2019)