We have just published a paper describing method and companion software for experimental validation of mutations with NGS (RNASeq) data:
Validation of predicted mRNA splicing mutations using high-throughput transcriptome data. Coby Viner, Stephanie N. Dorman, Ben C. Shirley, Peter K. Rogan. published in F1000Research ( http://f1000research.com/articles/3-8/v1 )
This approach fills a critical unmet need in genome-scale mutation analysis. Contact us if you want to trial the software.