VCF2Networks: applying genotype networks to single-nucleotide variants data

Dall'Olio, Giovanni Marco, 1983-; Vahdati, Ali R.; Bertranpetit, Jaume, 1952-; Wagner, Andreas; Laayouni, Hafid, 1968-

doi:http://dx.doi.org/10.1093/bioinformatics/btu650

VCF2Networks: applying genotype networks to single-nucleotide variants data

Citation

Dall'Olio GM, Vahdati AR, Bertranpetit J, Wagner A, Laayouni H. VCF2Networks: applying genotype networks to single-nucleotide variants data. Bioinformatics. 2015 Feb 1;31(3):438-9. DOI: 10.1093/bioinformatics/btu650

Abstract

SUMMARY: A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a representation of the set of genotypes associated with a single phenotype, and they allow one to estimate properties such as the robustness of the phenotype to mutations, and the ability of its associated genotypes to evolve new adaptations. So far, though, genotype networks analysis has rarely been applied to population genetics data. To help fill this gap, here we present VCF2Networks, a tool to determine and study genotype network structure from single-nucleotide variant data. AVAILABILITY AND IMPLEMENTATION: VCF2Networks is available at https://bitbucket.org/dalloliogm/vcf2networks. CONTACT: giovanni.dallolio@kcl.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.