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 in long-read RNA sequencing, identifying an average of 88 significant allele-specific splicing events per human sample.

• Why it matters: Understanding allele-specific splicing is crucial for insights into genetic regulation and disease mechanisms, but existing tools lack the accuracy and integration needed for long-read RNA data. This gap limits comprehensive analysis of transcript structure and genetic variation.
• What they did: The authors developed longcallR, a tool that performs joint SNP calling, haplotype phasing, and allele-specific analysis with high accuracy, and applied it to 202 human samples to assess its performance.
• The result: LongcallR identified an average of 88 significant allele-specific splicing events per sample, with 46% involving unannotated junctions, highlighting its potential to discover novel transcript variations.