SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads

Long-read RNA sequencing (lrRNA-seq) is a powerful technology to link transcript structures to genetic variants but such analysis is not often performed due to the lack of end-user tools. Here, we introduce longcallR for joint SNP calling, haplotype phasing, and allele-specific analysis, which achieves high accuracy on benchmark datasets. Applied to 202 human samples, longcallR identified 88 significant allele-specific splicing events per sample on average. 46% of them involved unannotated junctions.