I have a very simple question that, if I want to get the allele-specific expression of a gene from RNA-seq, what is the simplest way to do it. I know there are tools such as GATKAlleleCounter, but they are counting at each SNP sites, based on the vcf file. Thus if two or more SNPs are in one read, it will be counted multiple times if I simply add the count for each SNP within a gene body. Is there any tool that do the gene-level ASE aggregation? The phasing is known in my case. Thanks!