vcf_to_mixvir {MixviR}

Convert Sample VCF to MixviR Input Format

Description

Create data frame with relevant contents of VCF

Usage

vcf_to_mixvir(infile, max.vcf.size = 1e+08)

Arguments

infile

Path to a vcf file that must contain "DP" and "AD" flags in the FORMAT field.

max.vcf.size

Max memory usage (in bytes) allowed when reading in vcf file (from vcfR).

Value

Data frame with cols "CHR" "POS" "REF" "ALT" "DP" "REF_COUNT" "ALT_COUNT"

Examples

vcf_to_mixvir(infile = system.file("extdata", "vcfs", "Sample1_04182021.vcf.gz", package="MixviR"))