{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T08:03:53Z","timestamp":1770624233734,"version":"3.49.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/anntools.sourceforge.net\/<\/jats:p>\n               <jats:p>Contact: \u00a0vladimir.makarov@mssm.edu; chris.yoon@mssm.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts032","type":"journal-article","created":{"date-parts":[[2012,1,19]],"date-time":"2012-01-19T01:59:28Z","timestamp":1326938368000},"page":"724-725","source":"Crossref","is-referenced-by-count":39,"title":["AnnTools: a comprehensive and versatile annotation toolkit for genomic variants"],"prefix":"10.1093","volume":"28","author":[{"given":"Vladimir","family":"Makarov","sequence":"first","affiliation":[{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"}]},{"given":"Tina","family":"O'Grady","sequence":"additional","affiliation":[{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"}]},{"given":"Guiqing","family":"Cai","sequence":"additional","affiliation":[{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"}]},{"given":"Jayon","family":"Lihm","sequence":"additional","affiliation":[{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"}]},{"given":"Joseph D.","family":"Buxbaum","sequence":"additional","affiliation":[{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"}]},{"given":"Seungtai","family":"Yoon","sequence":"additional","affiliation":[{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"},{"name":"1 The Seaver Autism Center for Research and Treatment, 2Department of Psychiatry, 3Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5Department of Neuroscience, 6Department of Genetics and Genomic Sciences and 7The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,1,18]]},"reference":[{"key":"2023012512203234800_B1","doi-asserted-by":"crossref","first-page":"R661","DOI":"10.1016\/S0960-9822(99)80418-7","article-title":"CpG islands as genomic footprints of promoters that are associated with replication origins","volume":"9","author":"Antequera","year":"1999","journal-title":"Curr. Biol."},{"key":"2023012512203234800_B2","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1186\/1471-2164-11-293","article-title":"Ensembl variation resources","volume":"11","author":"Chen","year":"2010","journal-title":"BMC Genomics"},{"key":"2023012512203234800_B3","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1038\/nature08516","article-title":"Origins and functional impact of copy number variation in the human genome","volume":"464","author":"Conrad","year":"2010","journal-title":"Nature"},{"key":"2023012512203234800_B4","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512203234800_B5","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1093\/bioinformatics\/btr317","article-title":"SVA: software for annotating and visualizing sequenced human genomes","volume":"27","author":"Ge","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512203234800_B6","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1093\/bib\/bbn047","article-title":"Next generation tools for the annotation of human SNPs","volume":"10","author":"Karchin","year":"2009","journal-title":"Brief. Bioinform."},{"key":"2023012512203234800_B7","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1038\/ng.238","article-title":"Integrated detection and population-genetic analysis of SNPs and copy number variation","volume":"40","author":"McCarroll","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012512203234800_B8","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"2023012512203234800_B9","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/724\/48881294\/bioinformatics_28_5_724.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/724\/48881294\/bioinformatics_28_5_724.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:39:33Z","timestamp":1674661173000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/5\/724\/248883"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,18]]},"references-count":9,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2012,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts032","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,3,1]]},"published":{"date-parts":[[2012,1,18]]}}}