title: Population-based structural variation discovery with Hydra-Multi.
abstract: Current strategies for SNP and INDEL discovery incorporate sequence alignments from multiple individuals to maximize sensitivity and specificity. It is widely accepted that this approach also improves structural variant (SV) detection. However, multisample SV analysis has been stymied by the fundamental difficulties of SV calling, e.g. library insert size variability, SV alignment signal integration and detecting long-range genomic rearrangements involving disjoint loci. Extant tools suffer from poor scalability, which limits the number of genomes that can be co-analyzed and complicates analysis workflows. We have developed an approach that enables multisample SV analysis in hundreds to thousands of human genomes using commodity hardware. Here, we describe Hydra-Multi and measure its accuracy, speed and scalability using publicly available datasets provided by The 1000 Genomes Project and by The Cancer Genome Atlas (TCGA).
  
  
  METHODS
  Hydra-Multi is written in C++ and is freely available at https://github.com/arq5x/Hydra.
  
  
  BACKGROUND
  aaronquinlan@gmail.com or ihall@genome.wustl.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Lindberg
authors.affiliation: Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
authors.forename: Ira M
authors.initials: IM
authors.lastname: Hall
authors.affiliation: Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Quinlan
mesh_terms: D000818:Animals; D016208:Databases, Factual; D017353:Gene Deletion; D005828:Genetics, Population; D056914:Genomic Structural Variation; D023281:Genomics / Q000379:methods*; D006801:Humans; D006829:Hydra / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment; D012984:Software