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arXiv · 1401.2016

VCF2Networks: applying Genotype Networks to Single Nucleotide Variants data

Giovanni Marco Dall'Olio·Ali R. Vahdati·Bertranpetit Jaume·Wagner Andreas·Laayouni Hafid
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Abstract

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.

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Giovanni Marco Dall'Olio, Ali R. Vahdati, Bertranpetit Jaume, Wagner Andreas, Laayouni Hafid. 2014-01-09. VCF2Networks: applying Genotype Networks to Single Nucleotide Variants data. https://arxiv.org/abs/1401.2016

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