How to read vcf file in R

Question

I have this VCF format file, I want to read this file in R. However, this file contains some redundant lines which I want to skip. I want to get something like in the result where the row starts with the line matching #CHROM.

This is what I have tried:

chromo1<-try(scan(myfile.vcf,what=character(),n=5000,sep="\n",skip=0,fill=TRUE,na.strings="",quote="\"")) ## find the start of the vcf file
skip.lines<-grep("^#CHROM",chromo1)


column.labels<-read.delim(myfile.vcf,header=F,nrows=1,skip=(skip.lines-1),sep="\t",fill=TRUE,stringsAsFactors=FALSE,na.strings="",quote="\"")
num.vars<-dim(column.labels)[2]

myfile.vcf

    #not wanted line
    #unnecessary line
    #junk line
    #CHROM  POS     ID      REF     ALT
    11      33443   3        A       T
    12      33445   5        A       G

result

    #CHROM  POS     ID      REF     ALT
    11      33443   3        A       T
    12      33445   5        A       G

Solution 1

Maybe this could be good for you:

# read two times the vcf file, first for the columns names, second for the data
tmp_vcf<-readLines("test.vcf")
tmp_vcf_data<-read.table("test.vcf", stringsAsFactors = FALSE)

# filter for the columns names
tmp_vcf<-tmp_vcf[-(grep("#CHROM",tmp_vcf)+1):-(length(tmp_vcf))]
vcf_names<-unlist(strsplit(tmp_vcf[length(tmp_vcf)],"\t"))
names(tmp_vcf_data)<-vcf_names

p.s.: If you have several vcf files then you should use lapply function.

Best, Robert

Solution 2

data.table::fread reads it as intended, see example:

library(data.table)

#try this example vcf from GitHub
vcf <- fread("https://raw.githubusercontent.com/vcflib/vcflib/master/samples/sample.vcf")

#or if the file is local:
vcf <- fread("path/to/my/vcf/sample.vcf")

We can also use vcfR package, see the manuals in the link.

Comments

[Rich Scriven]

How about using a sequencing package? There are a few if you google "read vcf R"

[hrbrmstr]

Bioconductor has a few VCF readers.

[MAPK]

@RichardScriven that vcfreader is not appropriate in my case. I just want to skip the lines and get the tab separated table.

[Calimo]

Possible duplicate of Extract sample data from VCF files

[Ricardo Guerreiro]

Great answer, but do you always use points in your variable names? I find it confusing (especially if you also know python), prefer much more underscores. I guess it's a matter of taste though, cheers.

[Calimo]

@RicardoGuerreiro dots are idiomatic in variable names in R. Widely used and perfectly acceptable.