https://bioinformaticsonline.com/snippets/view/37688/plot-vcf-with-r? https://bioinformaticsonline.com/snippets/view/37688/plot-vcf-with-r Fri, 14 Sep 2018 05:44:46 -0500 https://bioinformaticsonline.com/snippets/view/37688/plot-vcf-with-r 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)]]> Jit