Personal Whole Genome Sequencing Variant Calls (SNPs, Indels, SVs, CNVs) of Manuel Corpas from Dante Labs 30x WGS

Overview This dataset contains high-confidence germline variant calls across all autosomes and sex chromosomes (chr1-22, chrX, chrY) from the whole genome sequencing (WGS) of Manuel Corpas, released as an open personal genomics resource under a CC0 1.0 Universal Public Domain Dedication. The data are provided for unrestricted use in research, education, and commercial applications. No liability is assumed by the data provider for any use of this dataset. Version 2 adds structural variant (SV) and copy number variant (CNV) calls using DELLY v1.7.3. Sequencing and Alignment Whole genome sequencing was performed by Dante Labs at approximately 30x mean coverage using Illumina short-read technology. Paired-end reads were aligned to the human reference genome GRCh37/hg19 (UCSC). SNP and Indel Calling (GATK 4) Variant discovery followed the GATK Best Practices workflow (GATK v4, Broad Institute): HaplotypeCaller: Per-chromosome GVCF generation in ERC mode, parallelised across 24 chromosomes on a 32-core Apple Mac Studio with 256 GB RAM. CombineGVCFs + GenotypeGVCFs: Merged and jointly genotyped across all chromosomes. Hard Filtering (GATK Best Practices for single-sample):SNPs: QD<2.0, FS>60.0, MQ<40.0, MQRankSum<-12.5, ReadPosRankSum<-8.0, SOR>3.0Indels: QD<2.0, FS>200.0, ReadPosRankSum<-20.0, SOR>10.0 SNP/Indel Statistics MetricSNP VCFIndel VCFTotal PASS variants3,716,648912,009Multiallelic sites8,83686,033Compressed file size166 MB48 MBMD572b728aefe54f9492b108c23ca7539bf0e173b22b24eb98b2193029ae65a2a8f SNP/Indel Quality Control QC MetricObservedExpected RangeStatusTi/Tv ratio2.032.0-2.1 (WGS)PASSHet/Hom ratio (SNPs)1.631.5-2.0 (outbred diploid)PASSTotal SNPs3,716,6483.5-4.0M (30x European)PASSTotal indels912,009800K-1.0MPASSGATK ValidateVariants0 errors0PASSMin QUAL score30.0≥30PASS Ti/Tv Ratio: 2.03, the most important QC metric for SNP calling. Values outside 2.0-2.1 for WGS indicate systematic errors. Het/Hom Ratio: 1.63, consistent with Southern European ancestry. Per-chromosome counts scale proportionally with chromosome size. chrY has 12,133 SNPs, consistent with a male sample. Structural Variant Calling (DELLY v1.7.3) Structural variants were called using DELLY v1.7.3 with paired-end and split-read analysis across all chromosomes. Five SV types were called in parallel: deletions (DEL), duplications (DUP), inversions (INV), translocations (BND), and insertions (INS). SV Statistics (PASS filter) SV TypeCountDeletions (DEL)5,854Translocations (BND)1,413Duplications (DUP)778Inversions (INV)673Insertions (INS)207Total PASS SVs8,925 SV Quality Control QC MetricObservedExpected RangeStatusTotal PASS SVs8,9255,000-25,000 (30x WGS)PASSDEL count5,8543,000-10,000PASSDUP count778200-2,000PASSINV count673100-1,500PASSBND count1,413500-5,000PASSINS count207100-1,000PASSPASS/Total ratio15% (8,925/60,016)10-30%PASS Deletion Size Distribution (PASS): <100 bp: 2,846; 100 bp-1 kb: 1,916; 1 kb-10 kb: 796; 10 kb-100 kb: 168; 100 kb-1 Mb: 60; >1 Mb: 68. The majority of deletions are small (<1 kb), consistent with known germline SV size distributions. Duplication Size Distribution (PASS): <1 kb: 311; 1 kb-10 kb: 185; 10 kb-100 kb: 153; 100 kb-1 Mb: 62; >1 Mb: 67. Copy Number Variant Calling (DELLY CNV v1.7.3) Read-depth based CNV calling was performed using DELLY CNV with GC-normalised read-depth analysis and a GRCh37 mappability map. SV breakpoints from the DELLY DEL calls were used for breakpoint refinement. CNV Statistics MetricValueTotal CNV calls1,387PASS CNVs873LowQual CNVs514PASS/Total ratio63% CNV Quality Control QC MetricObservedExpected RangeStatusTotal CNV calls1,387500-3,000 (30x WGS)PASSPASS CNVs873300-2,000PASSChromosomes covered23 (chr1-22, chrX)23 (chrY excluded)PASS CNV Size Distribution: <10 kb: 1,066; 10 kb-100 kb: 181; 100 kb-1 Mb: 80; >1 Mb: 60. The distribution is dominated by small CNVs, consistent with germline copy number variation patterns. CNV Per-Chromosome Distribution: Counts range from 20 (chr22) to 137 (chrX), with distribution broadly proportional to chromosome size. The elevated chrX count (137) relative to autosomes may reflect known CNV-enriched regions on the X chromosome. Files 15001711233855A.all_chroms.snp.vcf.gz - GATK hard-filtered PASS SNPs, all chromosomes (166 MB) 15001711233855A.all_chroms.indel.vcf.gz - GATK hard-filtered PASS indels, all chromosomes (48 MB) 15001711233855A.all_chroms.sv.pass.vcf.gz - DELLY PASS structural variants: DEL, DUP, INV, BND, INS (845 KB) 15001711233855A.all_chroms.cnv.vcf.gz - DELLY read-depth CNV calls, PASS + LowQual (93 KB) Sample Information Individual: Manuel Corpas (self-reported healthy adult male) Ancestry: Southern European (Spanish) Sample ID: 15001711233855A Sequencing provider: Dante Labs Sequencing date: November 2018 Coverage: ~30x mean depth Platform: Illumina short-read sequencing Technical Notes Reference genome: GRCh37/hg19 (UCSC). Coordinates are 1-based, chromosome-prefixed. SNP/Indel: Hard filtering used instead of VQSR (single-sample). SV: DELLY uses paired-end and split-read evidence. PASS filter applied by DELLY quality model. CNV: Read-depth based with GC correction using mappability map. Includes both PASS and LowQual calls for user filtering. Processing: Mac Studio 32-core, 256 GB RAM. SNPs/Indels: 4h19m. SVs: 51m. CNVs: 30m. Consent and Licence This dataset is released by Manuel Corpas with full informed consent as a voluntary act of personal genomic data sharing. It is dedicated to the public domain under the CC0 1.0 Universal Public Domain Dedication. You are free to copy, modify, distribute, and use the data for any purpose, including commercial applications, without asking permission. No warranties are provided. The data provider assumes no liability for any consequences arising from use of this data. Citation Corpas, M. (2026). Personal Whole Genome Sequencing Variant Calls (SNPs, Indels, SVs, CNVs) of Manuel Corpas from Dante Labs 30x WGS. Zenodo. https://doi.org/10.5281/zenodo.19285821## 数据集概述 本数据集包含来自曼努埃尔·科帕斯（Manuel Corpas）的全基因组测序（Whole Genome Sequencing, WGS）数据中的高置信度生殖系变异调用结果，覆盖所有常染色体与性染色体（chr1-22、chrX、chrY），作为开放个人基因组学资源以CC0 1.0 通用公共领域授权（CC0 1.0 Universal Public Domain Dedication）发布。本数据可无限制用于研究、教育及商业用途，数据提供者不对本数据集的任何使用承担责任。 版本2新增了使用DELLY v1.7.3生成的结构变异（Structural Variant, SV）与拷贝数变异（Copy Number Variant, CNV）调用结果。 ## 测序与比对 全基因组测序由Dante Labs采用Illumina短读长技术完成，平均测序深度约为30×。双端读数（Paired-end reads）比对至人类参考基因组GRCh37/hg19（UCSC）。 ## 单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与插入缺失变异（Insertion-Deletion, Indel）调用（GATK 4） 变异发现遵循GATK最佳实践流程（GATK v4，博德研究所（Broad Institute））： 1. **HaplotypeCaller**：以ERC模式生成每条染色体的GVCF文件，在配备256 GB内存的32核Apple Mac Studio上跨24条染色体并行运行。 2. **CombineGVCFs + GenotypeGVCFs**：合并所有染色体的GVCF文件并进行联合基因分型。 3. **硬过滤（GATK单样本最佳实践）**： - SNP过滤阈值：QD<2.0、FS>60.0、MQ<40.0、MQRankSum<-12.5、ReadPosRankSum<-8.0、SOR>3.0 - Indel过滤阈值：QD<2.0、FS>200.0、ReadPosRankSum<-20.0、SOR>10.0 ## SNP与Indel统计指标 | 指标 | SNP VCF文件 | Indel VCF文件 | |---------------------|-------------|---------------| | 合格（PASS）变异总数 | 3,716,648 | 912,009 | | 多等位基因位点 | 8,836 | 86,033 | | 压缩文件大小 | 166 MB | 48 MB | | MD5校验值 | 72b728aefe54f9492b108c23ca7539bf0e173b22b24eb98b2193029ae65a2a8f | - | ## SNP与Indel质量控制 | 质量控制指标 | 观测值 | 预期范围 | 状态 | |-------------|--------|----------|------| | Ti/Tv比值 | 2.03 | 2.0-2.1（全基因组测序） | PASS | | 杂合/纯合比值（SNP） | 1.63 | 1.5-2.0（远交二倍体） | PASS | | SNP总数 | 3,716,648 | 3.5-4.0M（30× 欧洲人群） | PASS | | Indel总数 | 912,009 | 800K-1.0M | PASS | | GATK ValidateVariants | 0错误 | - | PASS | | 最低QUAL值 | 30.0 | ≥30 | PASS | Ti/Tv比值为2.03，是SNP调用中最重要的质量控制指标，全基因组测序的Ti/Tv比值若超出2.0-2.1范围则提示存在系统性误差。Het/Hom比值为1.63，与南欧人群血统一致。每条染色体的变异计数与染色体大小成比例。chrY上存在12,133个SNP，与男性样本的特征一致。 ## 结构变异调用（DELLY v1.7.3） 采用DELLY v1.7.3通过双端读数与拆分读段分析对所有染色体进行结构变异调用，并行识别5类结构变异：缺失（DEL）、重复（DUP）、倒位（INV）、易位（BND）与插入（INS）。 ### 结构变异统计指标（PASS过滤后） | 结构变异类型 | 数量 | |--------------|------| | 缺失（DEL） | 5,854 | | 易位（BND） | 1,413 | | 重复（DUP） | 778 | | 倒位（INV） | 673 | | 插入（INS） | 207 | | 合格结构变异总数 | 8,925 | ### 结构变异质量控制 | 质量控制指标 | 观测值 | 预期范围 | 状态 | |-------------|--------|----------|------| | 合格结构变异总数 | 8,925 | 5,000-25,000（30× 全基因组测序） | PASS | | DEL计数 | 5,854 | 3,000-10,000 | PASS | | DUP计数 | 778 | 200-2,000 | PASS | | INV计数 | 673 | 100-1,500 | PASS | | BND计数 | 1,413 | 500-5,000 | PASS | | INS计数 | 207 | 100-1,000 | PASS | | PASS/总变异比值 | 15%（8,925/60,016） | 10-30% | PASS | 合格缺失变异大小分布：<100 bp：2,846；100 bp-1 kb：1,916；1 kb-10 kb：796；10 kb-100 kb：168；100 kb-1 Mb：60；>1 Mb：68。绝大多数缺失变异为小片段（<1 kb），与已知的生殖系结构变异大小分布一致。 合格重复变异大小分布：<1 kb：311；1 kb-10 kb：185；10 kb-100 kb：153；100 kb-1 Mb：62；>1 Mb：67。 ## 拷贝数变异调用（DELLY CNV v1.7.3） 采用DELLY CNV基于测序深度进行CNV调用，结合GC归一化测序深度分析与GRCh37基因组可映射性图谱。调用时使用DELLY DEL调用得到的结构变异断点进行断点优化。 ### 拷贝数变异统计指标 | 指标 | 数值 | |------|------| | 总CNV调用数 | 1,387 | | 合格CNV数 | 873 | | 低质量CNV数 | 514 | | PASS/总变异比值 | 63% | ### 拷贝数变异质量控制 | 质量控制指标 | 观测值 | 预期范围 | 状态 | |-------------|--------|----------|------| | 总CNV调用数 | 1,387 | 500-3,000（30× 全基因组测序） | PASS | | 合格CNV数 | 873 | 300-2,000 | PASS | | 覆盖染色体数 | 23（chr1-22、chrX） | 23（排除chrY） | PASS | 拷贝数变异大小分布：<10 kb：1,066；10 kb-100 kb：181；100 kb-1 Mb：80；>1 Mb：60。该分布以小片段CNV为主，符合生殖系拷贝数变异的典型模式。 拷贝数变异染色体分布：计数范围从chr22的20个到chrX的137个，分布与染色体大小大致成比例。chrX的计数（137）高于常染色体，这与X染色体上已知的CNV富集区域特征一致。 ## 数据文件 1. `15001711233855A.all_chroms.snp.vcf.gz`：经GATK硬过滤的合格SNP变异文件，覆盖所有染色体（166 MB） 2. `15001711233855A.all_chroms.indel.vcf.gz`：经GATK硬过滤的合格Indel变异文件，覆盖所有染色体（48 MB） 3. `15001711233855A.all_chroms.sv.pass.vcf.gz`：DELLY过滤得到的合格结构变异文件，包含DEL、DUP、INV、BND、INS五类变异（845 KB） 4. `15001711233855A.all_chroms.cnv.vcf.gz`：DELLY基于测序深度得到的CNV调用文件，包含合格与低质量两类变异（93 KB） ## 样本信息 - 个体：曼努埃尔·科帕斯（自我报告为健康成年男性） - 血统：南欧（西班牙裔） - 样本ID：15001711233855A - 测序服务商：Dante Labs - 测序日期：2018年11月 - 测序深度：约30×平均深度 - 测序平台：Illumina短读长测序平台 ## 技术说明 - 参考基因组：GRCh37/hg19（UCSC），坐标为1基坐标，染色体带前缀。 - SNP/Indel：采用硬过滤而非VQSR（单样本分析）。 - 结构变异：DELLY采用双端读数与拆分读段证据进行调用，PASS过滤由DELLY的质量模型自动完成。 - 拷贝数变异：基于测序深度，结合GC校正与可映射性图谱，包含合格与低质量两类变异供用户自行筛选。 - 处理硬件：Mac Studio 32核，256 GB内存。运行时间：SNP/Indel分析耗时4小时19分钟；结构变异分析耗时51分钟；拷贝数变异分析耗时30分钟。 ## 知情同意与授权 本数据集由曼努埃尔·科帕斯在完全知情同意的情况下发布，作为个人基因组数据共享的自愿行为。本数据集以CC0 1.0 通用公共领域授权，用户可自由复制、修改、分发并用于任何用途，包括商业用途，无需获得许可。本数据集不提供任何担保，数据提供者不对使用本数据产生的任何后果承担责任。 ## 引用格式 Corpas, M. (2026). Personal Whole Genome Sequencing Variant Calls (SNPs, Indels, SVs, CNVs) of Manuel Corpas from Dante Labs 30x WGS. Zenodo. https://doi.org/10.5281/zenodo.19285821