Prime

Type your tag names separated by a space and hit enter

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.

AVAILABILITY AND IMPLEMENTATION

Ferret tool and source code are publicly available at http://limousophie35.github.io/Ferret/

CONTACT

ferret@nih.gov

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Links

  • PMC Free PDF
  • PMC Free Full Text
  • Publisher Full Text
  • Authors+Show Affiliations

    ,

    Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA.

    ,

    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.

    Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA.

    Source

    Bioinformatics (Oxford, England) 32:14 2016 Jul 15 pg 2224-6

    MeSH

    Computational Biology
    Exome
    Gene Frequency
    Genetics, Population
    Genome, Human
    Genomics
    Haplotypes
    Humans
    INDEL Mutation
    Linkage Disequilibrium
    Polymorphism, Single Nucleotide
    Programming Languages
    Software
    User-Computer Interface

    Pub Type(s)

    Journal Article

    Language

    eng

    PubMed ID

    27153588

    Citation

    TY - JOUR T1 - Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project. AU - Limou,Sophie, AU - Taverner,Andrew M, AU - Winkler,Cheryl A, Y1 - 2016/03/18/ PY - 2015/08/14/received PY - 2016/03/14/accepted PY - 2016/5/7/entrez PY - 2016/5/7/pubmed PY - 2017/8/11/medline SP - 2224 EP - 6 JF - Bioinformatics (Oxford, England) JO - Bioinformatics VL - 32 IS - 14 N2 - UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: Ferret tool and source code are publicly available at http://limousophie35.github.io/Ferret/ CONTACT: ferret@nih.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. SN - 1367-4811 UR - https://www.unboundmedicine.com/medline/citation/27153588/Ferret:_a_user_friendly_Java_tool_to_extract_data_from_the_1000_Genomes_Project_ L2 - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw147 ER -