Hi,

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: chr1:27100181CGCA/C Numeric,3
chr1:43812234G/A Numeric,2

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?

You need one row per ALT, so just expand(input) first.