I am using GATK4 ASEReadCounter to create the inputs for an ASE analysis.
I understand that the inputs are pre-processed + mapped .bams, reference genome and a VCF for specific sites to be processed (As per GATK documentation).
I was wondering what the full function of the VCF file is in this program. Is ASEReadCounter solely using the vcf to determine which sites in the .bam to count or does it play other roles in the process that contributes to the output counts.
Any information would be amazingly helpful, thank you.