Hi, I'd recommend reading the paper "Tools and best practices for data processing in allelic expression analysis" suggested in the GATK ASEReadCounter website where it says:

...an easy to use tool in the widely used GATK v.3.4 [23, 24] called ASEReadCounter, which does not require any additional setup, and includes a variety of easily customizable read processing options as well as professional maintenance and documentation, similar to other GATK tools. Both operate on aligned RNA-seq reads and count the reference and alternative allele reads that passed filters for mapping and base quality at each bi-allelic heterozygous variant. The GATK tool offers several additional options for processing RNA-seq reads: by default each read fragment is counted only once if the base calls are consistent at the site of interest, and duplicate reads are filtered (see below). Other options allow filtering for coverage and for sites or reads with deletions...

Maybe you can find more information in the references of this paper.