RsQTL

RsQTL identifies splicing quantitative trait loci (sQTLs) by correlating variant allele fraction at expressed single nucleotide variant loci (VAF_RNA) with percent spliced in (PSI) values derived from RNA sequencing (RNA-seq) data.

Key Features:

• VAF_RNA–PSI Correlation Analysis: Correlates expressed SNVs with exon–exon junction usage to detect associations between allele-specific expression and differential intron excision.
• RNA-Seq–Only sQTL Detection: Identifies expressed sQTL loci without requiring matched DNA by leveraging transcriptome-derived VAF_RNA measurements.

Scientific Applications:

• Splicing Regulation Studies: Detects genetic variants influencing RNA splicing across tissues, supporting analysis of regulatory mechanisms and disease-associated splicing variation.

Methodology:

RsQTL computes VAF_RNA at expressed SNVs and PSI from local exon–exon junction reads, formats these data for association testing using the MatrixEQTL R package, and identifies significant correlations between genetic variation and splicing patterns.