Using the GATK's tools "haplotypecaller" and "ASEReadCounter" it is possible to produce a vcf file and a tabulated file for allele specific expression analysis (ASE), respectively.
The vcf file contains information about the number of reads mapping to each allele of a heterozygous position. I think this can be directly used for ASE.
If the vcf file contains allelic counts, why is there a tool specific for ASE?
Thank you in advance!