Hi, I have a very big vcf file (11.8 GB), the header and first row look like this:
#CHROM POS ID REF ALT QUAL FILTER INFO 1 13372 . G C 608.91 PASS "AC=3;AC_AFR=0;AC_AMR=0
How can I need access the #CHROM and POS columns?
Note that I cannot view it in excel because it's too big. I have also tries the following, but none worked:
#1 > library(VariantAnnotation) > vcfFile = system.file(package="VariantAnnotation", "extdata", "ExAC.r1.sites.vep.vcf.gz") > scanVcfHeader(vcfFile) Error in .io_check_exists(path(con)) : file(s) do not exist: '' #2 > vcf<-readVcf("ExAC.r1.sites.vep.vcf.gz","hg19") Error: cannot allocate vector of size 54 Kb
Any help is highly appreciated