Summary: Genotype networks are a method used in systems biology to study the innovability of a given phenotype, determining whether the phenotype is robust to mutations, and how do the genotypes associated to it are distributed in the genotype space. Here we developed VCF2Networks, a tool to apply this method to population genetics data, and in particular to single Nucleotide Variants data encoded in the Variant Call file Format (VCF). A complete summary of the properties of the genotype network that can be calculated by VCF2Networks is given in the Supplementary Materials 1. Availability and Implementation: The home page of the project is https://bitbucket.org/dalloliogm/vcf2networks . VCF2Networks is also available directly from the Python Package Index (PyPI), under the name vcf2networks.
@article{arxiv.1401.2016,
title = {VCF2Networks: applying Genotype Networks to Single Nucleotide Variants data},
author = {Giovanni Marco Dall'Olio and Ali R. Vahdati and Bertranpetit Jaume and Wagner Andreas and Laayouni Hafid},
journal= {arXiv preprint arXiv:1401.2016},
year = {2014}
}
Comments
5 pages, 1 table, plus supplementary of 7 pages and 5 figures