cisASE is a likelihood-based method for ASE detection at multiple levels(SNV,exon and gene). It takes matched DNA sequencing data as reference to reduce artifacts from technical bias and copy number variation to identify ASE due to cis-acting elements, and it works almost as well for dataset without DNA sequencing.
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cisASE: A likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data.
Liu Z, Gui T, Wang Z, Li H, Fu Y, Dong X, Li Y.
Bioinformatics. 2016 Jul 13. pii: btw416.