在R里面玩转vcf文件

library(vcfR)
vcf_file='/Users/jmzeng/germline/merge.dbsnp.vcf'
vcf <- read.vcfR( vcf_file, verbose = FALSE )

> vcf
***** Object of Class vcfR *****
39 samples
24 CHROMs
212,875 variants
Object size: 356.6 Mb
0 percent missing data
*****        *****         *****
> 

Objects of class vcfR can be manipulated with vcfR-method and extract.gt. 
Contents of the vcfR object can be visualized with the plot method. 

meta
character vector for the meta information
fix
matrix for the fixed information
gt
matrix for the genotype information

show(object) 
colnames(vcf@fix)
vcf@fix[1:4,1:4]
colnames(vcf@gt)
vcf@gt[1:4,1:4]

head(x, n = 6, maxchar = 80) 
plot(x, y, ...) ## 主要查看突变位点的质量值的分布情况  
x[i, j, samples = NULL, ..., drop]
dim(x) 
nrow(x)

pkg <- "pinfsc50"
vcf_file <- system.file("extdata", "pinf_sc50.vcf.gz", package = pkg)
dna_file <- system.file("extdata", "pinf_sc50.fasta", package = pkg)
gff_file <- system.file("extdata", "pinf_sc50.gff", package = pkg)
library(vcfR)
vcf <- read.vcfR( vcf_file, verbose = FALSE )
dna <- ape::read.dna(dna_file, format = "fasta")
gff <- read.table(gff_file, sep="\t", quote="")
library(vcfR)
chrom <- create.chromR(name='Supercontig', vcf=vcf, seq=dna, ann=gff)
plot(chrom)
chromoqc(chrom, dp.alpha=20)
chromoqc(chrom, xlim=c(5e+05, 6e+05))