library(vcfR)
# Input the files.
vcf <- read.vcfR("variant.vcf.gz", verbose = FALSE)
dna <- ape::read.dna("000000F_0.fa", format = "fasta")
#gff <- read.table(gff_file, sep="\t", quote="")
# Create a chromR object.
chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, verbose=TRUE)
plot(chrom)
chromoqc(chrom, dp.alpha=20)
