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

ABSTRACT: Long-read RNA sequencing is a powerful technology to link transcript structures to genetic variants, but this type of analysis is not often performed owing to the lack of end-user tools. Here we introduce longcallR for joint single-nucleotide polymorphism 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, of which 46% involved unannotated junctions.

SUBMITTER: Huang N 

PROVIDER: S-EPMC13041723 | biostudies-literature | 2026 Oct

REPOSITORIES: biostudies-literature