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

Huang, N.; Human Pangenome Reference Consortium,; Li, H.

doi:10.1101/2025.05.26.656191

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bioRxiv · 10.1101/2025.05.26.656191

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

Huang, N.·Human Pangenome Reference Consortium,·Li, H.

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Abstract

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.

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Huang, N., Human Pangenome Reference Consortium,, Li, H.. 2025-05-29. SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads. https://doi.org/10.1101/2025.05.26.656191

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