Hi

I have a vcf file for a gene. I am able to read it into R using readVcf() from the VariantAnnotation Bioconductor package.

I am interested to find how many variants are SNPs, how many are INDELS, and how many are SV.

This info is present in the info-VT field...

I am not able to subset the vcf based on the info-VT field.

Help appreciated..

Hi,

Extracting data and subsetting the VCF object is documented on ?readVcf and in the vignette, browseVignettes("VariantAnnotation"). There is also an example of filtering a vcf file on ?filterVcf. You may also look at the ?isSNV man page.

Extracting data is done with info(), geno(), alt(), ref(), etc. Using a sample file from the package,

> fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
> vcf <- readVcf(fl, "hg19")
> info(vcf)$DB
[1]  TRUE FALSE  TRUE FALSE FALSE

Subset 'vcf' on 'DB':

> dim(vcf) # original 
[1] 5 3
> dim(vcf[info(vcf)$DB])  # subset
[1] 2 3

Valerie