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

How about using a sequencing package? There are a few if you google "read vcf R" — Rich Scriven, Sep 11 '15 at 00:47
@RichardScriven that vcfreader is not appropriate in my case. I just want to skip the lines and get the tab separated table. — MAPK, Sep 11 '15 at 01:26
Possible duplicate of [Extract sample data from VCF files](https://stackoverflow.com/questions/21598212/extract-sample-data-from-vcf-files) — Calimo, Dec 21 '18 at 12:18

score 7 · Accepted Answer · edited Dec 21 '18 at 14:31

7

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

edited Dec 21 '18 at 14:31

Ricardo Guerreiro

497
1
4
17

answered Sep 11 '15 at 09:14

Róbert Herczeg

180
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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. – Ricardo Guerreiro Dec 21 '18 at 09:01
1

@RicardoGuerreiro dots are idiomatic in variable names in R. Widely used and perfectly acceptable. – Calimo Dec 21 '18 at 12:17

score 6 · Answer 2 · answered Jul 24 '18 at 09:05

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.

score 1 · Answer 3 · answered Jul 04 '22 at 14:48

1

Don't know how fread reads vcf correctly in comments above, but use 'skip' to define the first row start (or, if integer, amount of rows to skip).

library(data.table)
df = fread(file='some.vcf', sep='\t', header = TRUE, skip = '#CHROM')

answered Jul 04 '22 at 14:48

Jedi Knight

367
2
10

How to read vcf file in R

3 Answers3

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