
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
splicing, AbSplice
splicing, AbSplice
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