Ferret

Ferret extracts and processes variant data from the 1000 Genomes Project (1KG) to enable population genetic analysis and integration with downstream tools.

Key Features:

• Targeted Variant Retrieval: Extracts genotype data for single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from 1KG by locus, gene, or variant identifier.
• Allele Frequency Calculation: Computes population-specific allele frequencies within 1KG, with optional inclusion of Exome Sequencing Project data.
• Data Format Conversion: Converts 1KG data into PLINK- and HaploView-compatible formats to support linkage disequilibrium, haplotype inference, and tagSNP analysis.

Scientific Applications:

• Population Genomics and Association Studies: Enables analysis of human genetic variation, linkage disequilibrium patterns, haplotypes, and disease-associated loci across diverse populations.

Methodology:

Ferret accesses raw and annotated 1000 Genomes Project FTP data releases, extracts user-specified variants, computes allele frequencies, and reformats datasets for compatibility with established genetic analysis tools.