I am trying to convert Vcf files to VRanges objects. However, I get following Error message
readVcfAsVRanges(vcf1) Error in validObject(.Object) : invalid class "VRanges" object: 'refDepth' must be non-negative
I found this support post: https://stat.ethz.ch/pipermail/bioconductor/2014-June/060121.html. According to this I confirmed that I really have negative AD values in my vcf file. Following the instruction in the post I can circumvent this to still generate VRanges files. However, I am not completely sure what this negative AD value means and whether this is a problem. Can somebody help me with that? Under which condition can a negative AD value be generated?