Data supporting the manuscript "Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes"

This deposit contains the per-sample result data supporting the manuscript "Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes". Eight cancer cell lines (COLO829, H1437, H2009, H209, H2126, HCC1937, HCC1954, HG008) were analyzed against personalized, haplotype-resolved diploid reference genomes assembled with Verkko from the matched normal cell lines. For every sample the deposit provides: copynumber: haplotype-resolved copy-number profiles (tumor vs. normal read depth corrected by ploidy) point_mutation: somatic SNVs and indels (DeepSomatic) SV: somatic structural variants (nanomonsv) genomic_overview: genome overview including copynumber statuses, point mutations and structural variants assembly annotations: reference coordinate tables, misassembly regions, Liftoff gene models, segmental duplications, RepeatMasker, centromere/satellite annotation, and liftover chains to GRCh38 and CHM13 Sequencing data were obtained from the Castle-panel, SMaHT, and Cancer GIAB resources, and from in-house data collection. Clinical specimens analyzed during the project are not included in this deposit. See README.md for the full directory layout, file naming conventions, and column descriptions.