annotateVariant: Annotate the variants supplied in a VCF file

In ashishjain1988/VCFAnnotator-Tempus: VCFAnnotatorTempus

Description

This function annotates the variants by parsing VCF file supplied as input and call the Broad Institue's ExAC project API to get additional variant annotations.

Usage

annotateVariant(file)

Arguments

file	The path of the file containing the variant information in the VCF format

Value

The output is a dataframe object containing the annotation of the variants parsed from the VCF file and downloaded from the Broad Institute's ExAC Project. The annotation includes the chromosome, Postion, Variant Type, Depth of the reads, Alternate Allele Count, Percentage of Allele to Gentotype, Allele Frequency, Consequence.

Author(s)

Ashish Jain

Examples

library(VCFAnnotatorTempus)
VCFfilePath <- system.file('extdata', 'Challenge_data_test.vcf', package = 'VCFAnnotatorTempus')
t <- annotateVariant(file = VCFfilePath)
head(t)

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