FluentVCF is Bioconductor compliant, R package to determine the mutation type for a set of single nucleotide variants in a given genome.

Installation

Run the following lines in R to install FluentVCF:

if (!require("devtools")) {install.packages("devtools")}
devtools::install_github("mircomacchi/FluentVCF")

Then load the package:

library(FluentVCF)

Introduction

Variant Call Format (VCF) is a specification for storing genotype data in a tab-delimited file format. Below is a high-level diagram of a typical bioinformatics pipeline that produces a VCF file:

Features

FluentVCF is a package which takes:

1. a set of mutations (single nucleotide variants) in VCF format,

2. the corresponding reference genome (e.g., human genome hg38) and

3. a parameter “context_length” (see below) and determines for each mutation the corresponding mutation type as follows:

   The mutation type is “UP[REF>ALT]DOWN” where:

   • “REF>ALT” is the single nucleotide variant from REF base to ALT base, e.g., “C>T”
   • “UP” is upstream base from the reference genome (depending on the user parameter “context_length”)
   • “DOWN” is one or more downstream bases from the reference genome (same user parameter)

The package provides an additional function, “mut_summary”, which summarizes the mutation types for the set of mutations into a count table (number of mutations per mutation type).

Moreover, graphical outputs are integrated.

Requirements

FluentVCF relies on R packages to efficiently analyze and visualize variant call format (VCF) data. These dependencies include VariantAnnotation for VCF data extraction and annotation, GenomicRanges for genomic coordinate-based operations, dplyr for streamlined data manipulation, ggplot2 for creating informative plots, and RColorBrewer for aesthetically pleasing color palettes.

Dependencies installation

# Define the list of packages to be installed
required_packages <- c("VariantAnnotation", "GenomicRanges", "dplyr", "ggplot2", "RColorBrewer")

# Check if each package is already installed, and install if not
for (package in required_packages) {
  if (!requireNamespace(package, quietly = TRUE)) {
    install.packages(package, dependencies = TRUE)
  }
}

# Load the installed packages
library(VariantAnnotation)
library(GenomicRanges)
library(dplyr)
library(ggplot2)
library(RColorBrewer)

# You can now use FluentVCF with the required packages loaded