title: Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project.
abstract: 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's dataset, as well as visualize linkage disequilibrium pattern, infer haplotypes and design tagSNPs.
  
  
  
  Ferret tool and source code are publicly available at http://limousophie35.github.io/Ferret/
  
  
  
  ferret@nih.gov
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA.
authors.forename: Sophie
authors.initials: S
authors.lastname: Limou
authors.affiliation: Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA Quantitative and Computational Biology program, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Taverner
authors.affiliation: Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA.
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Winkler
mesh_terms: D019295:Computational Biology / Q000379:methods*; D059472:Exome; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods*; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D054643:INDEL Mutation; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface