AbSplice-DNA (hg19)

AbSplice-DNA predicts the probability that a variant causes aberrant splicing in a given tissue. See the publication: https://www.nature.com/articles/s41588-023-01373-3.
Here, we provide precomputed AbSplice-DNA scores for 49 human tissues and all possible SNVs genome-wide for hg19. This version contains 19,810 protein coding genes.

The folder 'AbSplice_DNA_hg19_snvs' contains all scores.
The folder 'AbSplice_DNA_hg19_snvs_high_scores' contains scores above 3 different cutoffs, which have approximately the same recalls as the high, medium and low cutoffs of SpliceAI: 

• high cutoff (0.2),
• medium cutoff (0.05),
• low cutoff (0.01).

AbSplice scores are tissue-specific. In case users require a single score we recommend to use the maximum AbSplice score across tissues.

AbSplice-DNA scores can be computed from custom VCF files (including indels) with the python package 'absplice': https://github.com/gagneurlab/absplice

The uploaded files contain the following columns (for longer description see README of github repository of AbSplice):

• Genomic coordinates of the variant:
  • chrom: Chromosome
  • pos: genomic position
  • ref: reference allele
  • alt: alternative allele
  • gene_id: Ensembl GeneID
• AbSplice_DNA_{tissue}: AbSplice score for the given tissue
• delta_logit_psi_{tissue}: MMSplice + SpliceMap score for a given tissue
• delta_psi_{tissue}: MMSplice + SpliceMap + Ψ_ref score for a given tissue
• splice_site_is_expressed_{tissue}: binary feature indicating if a splice site in the vicinity of the variant is expressed for a given tissue
• delta_score: SpliceAI Delta score (maximum of Delta score (acceptor/donor gain/loss))
• AbSplice_DNA_max: maximum AbSplice score across tissues for the given variant (this score is only provided in the files of the folder 'AbSplice_DNA_hg19_snvs_high_scores')

This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: https://github.com/Illumina/SpliceAI/tree/master