AbSplice-DNA (hg38)

<p>AbSplice-DNA predicts the probability that a variant causes aberrant splicing in a given tissue. See the publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a>.<br>Here, we provide precomputed AbSplice-DNA scores for 49 human tissues and all possible SNVs genome-wide for hg38. This version contains 19,713 protein coding genes.</p> <p>The folder 'AbSplice_DNA_hg38_snvs' contains all scores.<br>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 SpliceAI:&nbsp;</p> <ul> <li>high cutoff (0.2),</li> <li>medium cutoff (0.05),</li> <li>low cutoff (0.01).</li> </ul> <p>AbSplice scores are tissue-specific. In case users require a single score we recommend to use the maximum AbSplice score across tissues.</p> <p>AbSplice-DNA scores can be computed from custom VCF files (including indels)&nbsp;with the python package 'absplice': <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>The uploaded files contain the following columns (for longer description see README of <a href="https://github.com/gagneurlab/absplice">github repository of AbSplice</a>):</p> <ul> <li>Genomic coordinates of the variant: <ul> <li>chrom: Chromosome</li> <li>pos: genomic position</li> <li>ref: reference allele</li> <li>alt: alternative allele</li> <li>gene_id: Ensembl GeneID</li> </ul> </li> <li>AbSplice_DNA_{tissue}: AbSplice score for the given tissue</li> <li>delta_logit_psi_{tissue}: MMSplice + SpliceMap score for a given tissue</li> <li>delta_psi_{tissue}: MMSplice + SpliceMap + &Psi;_ref score for a given tissue</li> <li>splice_site_is_expressed_{tissue}: binary feature indicating if a splice site in the vicinity of the variant is expressed for a given tissue</li> <li>delta_score: SpliceAI Delta score (maximum of Delta score (acceptor/donor gain/loss))</li> <li>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')</li> </ul> <p>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:&nbsp;<a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>