I'm using the variantAnnotation package to read and subset my vcf file.
I'm using the following code in R on my input vcf to keep where where the AF is >= 3 percent.
inputfilteredaf <- subset(input, (geno(input)$AF) >= 0.03))
However, this leads to an error for variants that have multiple alleles: while a standard variant has just one AF value: chr1:27100179_CCCG/C 0.014
The AF value for a multiple-allele variant is this:
The error that I get is: Error in eval(expr, as.env(envir, enclos)) : (list) object cannot be coerced to type 'double'
How can this be solved?