AbSplice2-DNA (hg38)

AbSplice2-DNA predicts the probability that a variant causes aberrant splicing in a given tissue. See the publication: [link to biorxiv]. AbSplice2 is an updated version of AbSplice that we published earlier: https://www.nature.com/articles/s41588-023-01373-3.Here, we provide precomputed AbSplice2-DNA scores for 49 human tissues and all possible SNVs genome-wide for hg38. This version contains 19,274 protein coding genes. The folder 'AbSplice_DNA_hg38_snvs' contains all scores.The folder 'AbSplice_DNA_hg38_snvs_high_scores' contains scores above 3 different cutoffs, which have approximately the same recalls as the high, medium and low cutoffs of Pangolin: high cutoff (0.2), medium cutoff (0.1), low cutoff (0.05). AbSplice scores are tissue-specific. In case users require a single score we recommend to use the maximum AbSplice score across tissues. AbSplice2-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 gain_score: One of the the two scores predicted by Pangolin. The score represents probability of the variant causing an increase in splicing level loss_score: One of the the two scores predicted by Pangolin. The score represents probability of the variant causing an decrease in splicing level 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_hg38_snvs_high_scores')