SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.
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- Record sourced from PubMed, PMID 41912802.
- Also identified by DOI 10.1038/s41592-026-03045-6 and PMC identifier 13041723.
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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.