Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants

MOTIVATION: In silico prediction tools are essential for identifying variants which create or disrupt cis splicing motifs. However, there are limited options for genome-scale discovery of splice-altering variants. RESULTS: We have developed Spliceogen, a highly scalable pipeline integrating predictions from some of the individually best performing models for splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer. AVAILABILITY: Spliceogen is available as a command line tool which accepts VCF/BED inputs and handles both single nucleotide variants (SNVs) and indels (https://github.com/VCCRI/Spliceogen). SNV databases with prediction scores are also available, covering all possible SNVs at all genomic positions within all Gencode-annotated multi-exon transcripts (https://github.com/VCCRI/Spliceogen/tree/master/database). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.