Introduction

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.govSupplementary data are available at Bioinformatics online.

Publications

  1. Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project.
    Cite this
    Limou S, Taverner AM, Winkler CA, 2016-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Sophie Limou
    Developer

    Molecular Genetic Epidemiology Section, Basic Research Laboratory, United States of America

  2. Andrew M Taverner
    Developer

    Molecular Genetic Epidemiology Section, Basic Research Laboratory, United States of America

  3. Cheryl A Winkler
    Investigator

    Molecular Genetic Epidemiology Section, Basic Research Laboratory, United States of America

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Summary
AccessionBT006622
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByCheryl A Winkler