title: AnnTools: a comprehensive and versatile annotation toolkit for genomic variants.
abstract: AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization of the coding variants, AnnTools searches for overlaps with regulatory elements, disease/trait associated loci, known segmental duplications and artifact prone regions, thereby offering an integrated and comprehensive analysis of genomic data. The tool conveniently accepts user-provided tracks for custom annotation and offers flexibility in input data formats. The output is generated in the universal Variant Call Format. High annotation speed makes AnnTools suitable for high-throughput sequencing facilities, while a low-memory footprint and modest CPU requirements allow it to operate on a personal computer. The application is freely available for public use; the package includes installation scripts and a set of helper tools.
  
  
  BACKGROUND
  http://anntools.sourceforge.net/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: The Seaver Autism Center for Research and Treatment, Department of Psychiatry, Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA. vladimir.makarov@mssm.edu
authors.forename: Vladimir
authors.initials: V
authors.lastname: Makarov
authors.forename: Tina
authors.initials: T
authors.lastname: O'Grady
authors.forename: Guiqing
authors.initials: G
authors.lastname: Cai
authors.forename: Jayon
authors.initials: J
authors.lastname: Lihm
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Buxbaum
authors.forename: Seungtai
authors.initials: S
authors.lastname: Yoon
mesh_terms: D056915:DNA Copy Number Variations; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D012984:Software