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

Sophie Limou¹, Andrew M Taverner², Cheryl A Winkler¹

¹Molecular Genetic Epidemiology Section, Basic Research Laboratory, Basic Science Program, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA.

Bioinformatics (Oxford, England)

|May 7, 2016

Summary

Ferret is a Java tool that simplifies accessing and analyzing human genetic variation data from the 1000 Genomes Project. It enables researchers to easily extract, compute frequencies, and visualize genetic data for various populations.

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Area of Science:

Genomics
Bioinformatics
Population Genetics

Background:

The 1000 Genomes Project offers extensive human genetic variation data.
Accessing and analyzing this large dataset can be complex for researchers.

Purpose of the Study:

To develop a user-friendly tool, Ferret, for simplified access and analysis of 1000 Genomes Project data.
To facilitate the manipulation, exploration, and integration of genetic variation data.

Main Methods:

Ferret is a Java-based tool designed for extracting genetic variation information.
It retrieves genotype data for SNPs and indels from the 1000 Genomes Project.
Computes allelic frequencies for specified populations and converts data for use with other bioinformatics tools.

Main Results:

Ferret allows easy extraction of genetic variation data from large files.
It computes allelic frequencies for 1000 Genomes Project and Exome Sequencing Project populations.
The tool facilitates data merging, linkage disequilibrium visualization, haplotype inference, and tagSNP design.

Conclusions:

Ferret provides a straightforward method for researchers, including non-bioinformaticians, to utilize 1000 Genomes Project data.
It enhances the accessibility and utility of human genetic variation resources for diverse research applications.