Why does ASEReadCounter require a reference genome? Surely all the information necessary is in the VCF and the RNA-seq reads?
Is there any documentation that specifically describes the ASECounter algorithm?
Then, you might try looking at the code. I think that's all we have for documentation on the tool.
Because ASEReadCounter is a GATK tool, it requires a reference. (All GATK tools require a reference). You can read more about the tool in the paper or in the GATK tool documentation.
The paper doesn't describe the ASEreadcounter algorithm at all.