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
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