Read in SNPs from a VCF — read

Helper function to read in SNP data from a VCF file.

Usage

read_vcf(file, bsgenome)

Arguments

file: File path to a VCF file. See details.
bsgenome: An object of class BSgenome for the species you are interrogating; see BSgenome::available.genomes for a list of species.

Value

A GRanges object containing SNP_id, REF, and ALT columns.

Details

Note that the VCF must be filtered to only contain variant sites (i.e., no 0/0), or only homozygous alt sites if you choose (0/1 or 1/1). This can be accomplished with bcftools:

# Filter to any variant sites:
bcftools view -i 'GT="alt"' ...
# Filter to homozygous alt sites:
bcftools view -i 'GT="AA"' ...

Examples

if (FALSE) {
library(BSgenome.Ggallus.UCSC.galGal6)
vcf_file <- system.file("extdata", "galGal6-chr33.vcf.gz", package="tfboot", mustWork = TRUE)
snps <- read_vcf(vcf_file, BSgenome.Ggallus.UCSC.galGal6)
snps
}