RsQTL: correlation of expressed SNVs with splicing using RNA-sequencing data

Summary RsQTL is a tool for identification of splicing quantitative trait loci (sQTLs) from RNA-sequencing (RNA-seq) data by correlating the variant allele fraction at expressed SNV loci in the transcriptome (VAF RNA ) with the proportion of molecules spanning local exon-exon junctions at loci with differential intron excision (percent spliced in, PSI). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression Project (GTEx). RsQTL does not require matched DNA and can identify a subset of expressed sQTL loci. Due to the dynamic nature of VAF RNA , RsQTL is applicable for the assessment of conditional and dynamic variation-splicing relationships. Availability and implementation https://github.com/HorvathLab/RsQTL . Contact [email protected] or [email protected] Supplementary Information RsQTL_Supplementary_Data.zip