query_vcf: Query VCF Data

In AndersenLab/cegwas: A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.

Description

query_vcf enables you to query variants within a VCF

Usage

query_vcf(..., info = c(), format = c("TGT"), impact = c("MODERATE",
  "HIGH"), samples = "ALL", long = TRUE, vcf = get_vcf())

Arguments

...	Gene names, regions, or wormbase identifiers to query.
info	Info columns to output. If an ANN (annotation) column is available it is automatically fetched. [Default c()]
samples	A set of samples to subset on [default: "ALL"]
long	Return dataset in long or wide format. [Default TRUE]
vcf	Use a custom VCF.

Value

Dataframe with variant data

Examples

query_vcf("pot-2","II:1-10000","WBGene00010785")

AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.