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

LongcallR enables highly accurate SNP calling, haplotype phasing, and allele-specific analysis from long-read RNA sequencing, revealing an average of 88 allele-specific splicing events per human sample.

• Why it matters: Understanding allele-specific splicing is crucial for insights into genetic regulation and disease mechanisms, yet existing tools lack the precision for long-read RNA data. Addressing this gap allows for more comprehensive transcriptome analysis and discovery of novel splicing events.
• What they did: The authors developed longcallR, a tool that performs joint SNP calling, haplotype phasing, and allele-specific analysis, validated on benchmark datasets and applied to 202 human samples.
• The result: LongcallR identified numerous allele-specific splicing events, with nearly half involving previously unannotated junctions, enabling deeper exploration of transcript diversity and genetic regulation.