{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T17:20:00Z","timestamp":1758820800772},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The 1000 Genomes (1KG) Project provides a near-comprehensive resource on human genetic variation in worldwide reference populations. 1KG variants can be accessed through a browser and through the raw and annotated data that are regularly released on an ftp server. We developed Ferret, a user-friendly Java tool, to easily extract genetic variation information from these large and complex data files. From a locus, gene(s) or SNP(s) of interest, Ferret retrieves genotype data for 1KG SNPs and indels, and computes allelic frequencies for 1KG populations and optionally, for the Exome Sequencing Project populations. By converting the 1KG data into files that can be imported into popular pre-existing tools (e.g. PLINK and HaploView), Ferret offers a straightforward way, even for non-bioinformatics specialists, to manipulate, explore and merge 1KG data with the user\u2019s dataset, as well as visualize linkage disequilibrium pattern, infer haplotypes and design tagSNPs.<\/jats:p>\n               <jats:p>Availability and implementation: Ferret tool and source code are publicly available at http:\/\/limousophie35.github.io\/Ferret\/.<\/jats:p>\n               <jats:p>Contact: \u00a0ferret@nih.gov<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw147","type":"journal-article","created":{"date-parts":[[2016,3,19]],"date-time":"2016-03-19T01:40:00Z","timestamp":1458351600000},"page":"2224-2226","source":"Crossref","is-referenced-by-count":8,"title":["Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project"],"prefix":"10.1093","volume":"32","author":[{"given":"Sophie","family":"Limou","sequence":"first","affiliation":[{"name":"1 Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA"}]},{"given":"Andrew M.","family":"Taverner","sequence":"additional","affiliation":[{"name":"1 Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA"},{"name":"2 Quantitative and Computational Biology program, Princeton University, Princeton, NJ 08544, USA"}]},{"given":"Cheryl A.","family":"Winkler","sequence":"additional","affiliation":[{"name":"1 Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,3,18]]},"reference":[{"key":"2023020112454142200_btw147-B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"1000 Genomes Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2023020112454142200_btw147-B2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","article-title":"Haploview: analysis and visualization of LD and haplotype maps","volume":"21","author":"Barrett","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020112454142200_btw147-B3","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":"2023020112454142200_btw147-B4","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1016\/j.ajhg.2013.08.006","article-title":"Actionable, pathogenic incidental findings in 1,000 participants' exomes","volume":"93","author":"Dorschner","year":"2013","journal-title":"Am. 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Genet"},{"key":"2023020112454142200_btw147-B5","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1093\/bioinformatics\/btq671","article-title":"Tabix: fast retrieval of sequence features from generic TAB-delimited files","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020112454142200_btw147-B6","doi-asserted-by":"crossref","first-page":"D52","DOI":"10.1093\/nar\/gkq1237","article-title":"Entrez Gene: gene-centered information at NCBI","volume":"39","author":"Maglott","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020112454142200_btw147-B7","doi-asserted-by":"crossref","unstructured":"NCBI Resource Coordinators (2014) Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., 42, D7\u2013D17.","DOI":"10.1093\/nar\/gkt1146"},{"key":"2023020112454142200_btw147-B8","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. 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