Datasets supporting AbsCNV for pairwise copy-number variation analysis of aneuploid genomes

This dataset accompanies the AbsCNV study on read-depth-based copy-number analysis and pairwise detection of copy-number differences between aneuploid genomes. It provides processed inputs, simulation truth sets, CNV predictions, fitted model parameters, and evaluation results supporting the analyses presented in the manuscript. The dataset includes: 1. A controlled three-sample workflow example, with normalized and smoothed read depth, Gaussian mixture model parameters, breakpoint scores, shared genomic segments, copy-number assignments, and pairwise comparison results. 2. Single-sample and paired-sample benchmarks, including absolute copy-number profiles, benchmark truth, native and standardized predictions from the compared tools, and event-level and base-level performance metrics. 3. Six CNV-length experiments covering 20, 50, 100, 200, 500, and 1,000 kb, with simulation designs, read-depth inputs, truth sets, filtered predictions, and evaluation summaries. 4. Public WGS analyses of FASR, MCF7, and TAMR, including read-depth inputs, fitted models, pairwise CNV calls, histogram parameters, published LUMPY structural-variant calls, and overlap-based support summaries. 5. U251 clonal-lineage analyses, including read-depth inputs from ten samples, absolute copy-number assignments, filtered pairwise CNV calls, and interval-based lineage summaries. The files are distributed in datasets.zip, which preserves the directory structure. Each main data directory contains an English README describing its files, their provenance or generating scripts, and downstream uses. The accompanying top-level README provides an overview and instructions for using the data. The two shared Sample_A read-depth files correspond to the same absolute copy-number profile but different simulated-read realizations. They are retained separately to preserve the inputs used in the respective benchmark analyses. Associated software: https://github.com/AqduanCode/AbsCNV Source sequencing accessions: GSE118715 for the public WGS data and OMIX015037 for the U251 sequencing data.