title: Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
abstract: : We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios.
  
  
  
  Manta is released under the open-source GPLv3 license. Source code, documentation and Linux binaries are available from https://github.com/Illumina/manta.
  
  
  
  csaunders@illumina.com
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Illumina, Inc, 5200 Illumina Way, San Diego, CA 92122, USA and.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Chen
authors.affiliation: Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors.forename: Ole
authors.initials: O
authors.lastname: Schulz-Trieglaff
authors.affiliation: Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Shaw
authors.affiliation: Illumina, Inc, 5200 Illumina Way, San Diego, CA 92122, USA and.
authors.forename: Bret
authors.initials: B
authors.lastname: Barnes
authors.affiliation: Illumina, Inc, 5200 Illumina Way, San Diego, CA 92122, USA and.
authors.forename: Felix
authors.initials: F
authors.lastname: Schlesinger
authors.affiliation: Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors.forename: Morten
authors.initials: M
authors.lastname: Källberg
authors.affiliation: Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Cox
authors.affiliation: Illumina, Inc, 5200 Illumina Way, San Diego, CA 92122, USA and.
authors.forename: Semyon
authors.initials: S
authors.lastname: Kruglyak
authors.affiliation: Illumina, Inc, 5200 Illumina Way, San Diego, CA 92122, USA and.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Saunders
mesh_terms: D004273:DNA, Neoplasm; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D009369:Neoplasms / Q000235:genetics*; D012984:Software
chemical_list: D004273:DNA, Neoplasm