In ashishjain1988/VCFAnnotator-Tempus: VCFAnnotatorTempus

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VCFAnnotator

This is an R package for the automatic annotation generation of the variants supplied in the VCF file into a text file.

Requirement

You need R version 3.5.1 or above to run this application. Other dependencies are:

• tidyverse (>= 1.2.1)
• ensurer (>= 1.1.0)
• httr (>= 1.3.1)
• jsonlite (>=1.6.0)

How to install the R package

• Install Dependencies

install.packages(c("tidyverse","ensurer","httr","jsonlite"))

From Github

install.packages("devtools")
library("devtools")
install_github("ashishjain1988/VCFAnnotator")

From tar file

install.packages("<Absolute Path>/VCFAnnotator_1.0.0.tar.gz", repos = NULL)

Running the VCF Annotator

VCF Annotator is an R package used for the automatic annotation generation of the variants supplied in the VCF file. This package parses information of variants supplied in a VCF file. This package also add the annotations from the Broad Institue's ExAC project by making a POST call to its batch API. The output in the text file have the annotations including

• Type of variation (most deleterious)
• Depth of sequence coverage
• Number of reads supporting variants
• Percentage of reads supporting the variant versus those supporting reference reads
• Allele frequency from ExAC project
• Consequence of the variant from ExAC project

In our code, we rank the type of variations according to the magnitude of its deleterious possibilty (Insertion,Deletion > Complex > Multi Nucleotide Polymorphism > Single Nucleotide Polymorphism). In order to annotate the variants supplied in the VCF file annotateVariant function of this package is used. This function requires the path of the VCF file and then automatically annotates the variants and supply them in a data.frame object which can be written into a text file. A simple example is shown below by using an R terrminal.

library(VCFAnnotator)

VCFfilePath <- system.file('extdata', 'Challenge_data.vcf', package = 'VCFAnnotator')
t <- annotateVariant(file = VCFfilePath)
write.table(t,"Challenge_data_annotated_variants.txt",sep="\t",quote = F,row.names = F)

In addition to that, there is another function getVariantInfoFromExACAPI which make a batch call to the Broad Institue's ExAC project API to retreive the annotation information of variants. More information about this function can be found by typing ?getVariantInfoFromExACAPI in R terminal. This function is called by the annotateVariant function internally to add annotations from ExAC project.

ashishjain1988/VCFAnnotator-Tempus documentation built on Feb. 3, 2021, 3:18 a.m.