Motivation: RNA-seq has been widely used to study the transcriptome. Comparing to microarray, sequencing-based RNA-seq is able to identify splicing variants and single nucleotide variants in one experiment simultaneously. This provides unique opportunity to detect variants that associated with aberrant splicing. Despite the popularity of RNA-seq, no bioinformatics tool has been developed to leverage this advantage to identify variants associated with aberrant splicing.

Results: We have developed PVAAS, a tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. PVAAS works in three steps: (i) identify aberrant splicings; (ii) use user-provided variants or perform variant calling; (iii) assess the significance of association between variants and aberrant splicing events.

Availability and implementation: PVAAS is written in Python and C. Source code and a comprehensive user’s manual are freely available at: http://pvaas.sourceforge.net/.

Contact: wang.liguo@mayo.edu or kocher.jeanpierre@mayo.edu

Supplementary information: Supplementary data are available at Bioinformatics online.