SNPlice

SNPlice is a computational tool that identifies variants that modulate intron retention from RNA-seq data. SNPlice mines RNA-seq data to detect reads spanning single-nucleotide variants (SNVs) and nearby splice junctions and assesses the co-occurrence of variants and molecules that remain unspliced at nearby exon-intron boundaries. Allele-specific sequencing illustrates the co-occurrence of variant nucleotides and exon-intron boundaries. SNPlice results generally agree with those of other splice-prediction tools, yet can also identify splice-modulating elements missed by them. SNPlice can be used to identify variants associated with unexpected splicing events and to measure the splice-modulating potential of canonical splice-site SNVs.