VCF2Networks: applying Genotype Networks to Single Nucleotide Variants data

TL;DR

VCF2Networks is a new tool that applies genotype network analysis to population genetics data, specifically single nucleotide variants in VCF files, enabling detailed study of phenotype robustness and genotype distribution.

Contribution

It introduces VCF2Networks, a novel software that adapts genotype network analysis to VCF data, expanding its application in population genetics research.

Findings

Enables analysis of genotype networks from VCF data

Provides comprehensive network properties calculation

Facilitates studying phenotype robustness in populations

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.