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')AbSplice2-DNA 可预测变异在特定组织中引发异常剪接的概率。相关研究详见预印本链接：[link to biorxiv]。AbSplice2 是我们此前发表的 AbSplice 的更新版本，原文刊载于：https://www.nature.com/articles/s41588-023-01373-3。 本次发布的数据集中，我们提供了针对 hg38 人类参考基因组全基因组范围内所有可能的单核苷酸变异（SNV），以及 49 种人体组织的预计算 AbSplice2-DNA 评分。本数据集包含 19274 个蛋白质编码基因。 文件夹"AbSplice_DNA_hg38_snvs"包含全部评分数据。文件夹"AbSplice_DNA_hg38_snvs_high_scores"则包含三类不同截断值以上的评分，这三类截断值的召回率分别与 Pangolin 的高、中、低截断值相当：高截断值（0.2）、中截断值（0.1）、低截断值（0.05）。 AbSplice 评分具有组织特异性。若用户需要单一评分，我们建议使用该变异在所有组织中的最大 AbSplice 评分。 用户可通过 Python 工具包"absplice"（https://github.com/gagneurlab/absplice）基于自定义 VCF 文件（包含插入缺失变异）计算 AbSplice2-DNA 评分。 本次上传的文件包含以下列（详细说明请参见 AbSplice GitHub 仓库的 README 文档）： 变异的基因组坐标： - chrom：染色体编号 - pos：基因组位置 - ref：参考等位基因 - alt：替代等位基因 - gene_id：Ensembl 基因ID AbSplice_DNA_{tissue}：对应组织的 AbSplice 评分 delta_logit_psi_{tissue}：针对特定组织的 MMSplice + SpliceMap 评分 delta_psi_{tissue}：针对特定组织的 MMSplice + SpliceMap + Ψ_ref 评分 gain_score：Pangolin 预测的两类评分之一，代表变异导致剪接水平升高的概率 loss_score：Pangolin 预测的两类评分之一，代表变异导致剪接水平降低的概率 AbSplice_DNA_max：该变异在所有组织中的最大 AbSplice 评分（该评分仅在"AbSplice_DNA_hg38_snvs_high_scores"文件夹的文件中提供）