Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project | Zendy

Sophie Limou | Zendy; Andrew M. Taverner | Zendy; Cheryl A. Winkler | Zendy

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Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project

Author(s) -

Sophie Limou,

Andrew M. Taverner,

Cheryl A. Winkler

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw147

Subject(s) - java , computer science , 1000 genomes project , file transfer protocol , source code , indel , human genetic variation , genome , biology , single nucleotide polymorphism , the internet , human genome , world wide web , genotype , genetics , gene , operating system

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.

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