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Manuel Corpas全基因组测序（Whole Genome Sequencing, WGS）的、覆盖所有常染色体与性染色体（chr1-22、chrX、chrY）的高置信度生殖系变异调用结果，以开放个人基因组资源的形式基于CC0 1.0 通用公共领域贡献协议发布。本数据集可无限制用于研究、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。 ## V2版本更新 V2版本新增了使用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 本全基因组测序由Dante Labs采用Illumina短读长技术完成，平均覆盖度约为30×。双端测序reads比对至人类参考基因组GRCh37/hg19（UCSC）。 # 单核苷酸多态性与插入缺失调用（GATK 4） 变异发现流程遵循GATK最佳实践规范（GATK v4，博德研究所）： 1. **HaplotypeCaller**：以ERC模式生成每条染色体的GVCF文件，在配备256GB内存的32核Apple Mac Studio上对24条染色体并行处理。 2. **CombineGVCFs + GenotypeGVCFs**：对所有染色体的结果进行合并与联合基因分型。 3. **硬过滤（单样本GATK最佳实践）**： - 单核苷酸多态性（SNP）过滤阈值：QD<2.0、FS>60.0、MQ<40.0、MQRankSum<-12.5、ReadPosRankSum<-8.0、SOR>3.0 - 插入缺失（Indel）过滤阈值：QD<2.0、FS>200.0、ReadPosRankSum<-20.0、SOR>10.0 ## SNP/Indel 统计指标 | 统计指标 | SNP VCF文件 | Indel VCF文件 | |-------------------------|-------------|---------------| | 合格（PASS）变异总数 | 3,716,648 | 912,009 | | 多等位基因位点数量 | 8,836 | 86,033 | | 压缩文件大小 | 166 MB | 48 MB | | MD5校验值 | 72b728aefe54f9492b108c23ca7539bf0e173b22b24eb98b2193029ae65a2a8f | - | ## SNP/Indel 质量控制 | 质量控制指标 | 观测值 | 预期范围 | 质控状态 | |-----------------------------|----------|-----------------------------------|----------| | 转换/颠换比（Ti/Tv ratio） | 2.03 | 2.0-2.1（全基因组测序场景） | PASS | | 杂合/纯合比值（SNP） | 1.63 | 1.5-2.0（远交二倍体样本） | PASS | | SNP总数 | 3,716,648| 3.5-4.0M（30× 欧洲血统样本） | PASS | | Indel总数 | 912,009 | 800K-1.0M | PASS | | GATK ValidateVariants结果 | 0错误 | 0错误 | PASS | | 最低QUAL值 | 30.0 | ≥30 | PASS | 注：转换/颠换比（Ti/Tv ratio）是SNP Calling中最重要的质控指标，全基因组测序场景下该值若超出2.0-2.1范围则提示存在系统性错误。本次观测值为2.03，符合要求。杂合/纯合比值为1.63，与南欧血统特征一致。各染色体的变异计数与染色体大小呈正比，chrY包含12,133个SNP，与男性样本特征相符。 # 结构变异调用（DELLY v1.7.3） 本数据集使用DELLY v1.7.3，通过双端测序与分裂读长分析对所有染色体进行结构变异（Structural Variant, SV）调用。并行识别5类结构变异：缺失（Deletions, DEL）、重复（Duplications, DUP）、倒位（Inversions, INV）、易位（Translocations, BND）与插入（Insertions, INS）。 ## 结构变异统计（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 | 质控状态 | |-----------------------------|----------------------|-----------------------------------|----------| | 合格结构变异总数 | 8,925 | 5,000-25,000（30× 全基因组测序） | PASS | | 缺失变异（DEL）数量 | 5,854 | 3,000-10,000 | PASS | | 重复变异（DUP）数量 | 778 | 200-2,000 | PASS | | 倒位变异（INV）数量 | 673 | 100-1,500 | PASS | | 易位变异（BND）数量 | 1,413 | 500-5,000 | PASS | | 插入变异（INS）数量 | 207 | 100-1,000 | PASS | | 合格变异占总变异比例 | 15%（8,925/60,016） | 10-30% | PASS | **缺失变异大小分布（PASS过滤后）**：<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。大部分缺失变异为小片段（<1 kb），与已知生殖系结构变异的大小分布特征一致。 **重复变异大小分布（PASS过滤后）**：<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） 本数据集使用DELLY CNV，基于GC校正的读长深度分析与GRCh37基因组可映射性图谱进行基于读深度的拷贝数变异（Copy Number Variant, CNV）调用，并使用DELLY DEL调用得到的结构变异断点进行断点优化。 ## CNV 统计指标 | 统计指标 | 数值 | |-------------------------|---------| | 总CNV调用数 | 1,387 | | 合格（PASS）CNV数 | 873 | | 低质量CNV数 | 514 | | 合格变异占比 | 63% | ## CNV 质量控制 | 质量控制指标 | 观测值 | 预期范围 | 质控状态 | |-----------------------------|------------------------------------------|-----------------------------------|----------| | 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 | | 覆盖的染色体数量 | 23条（chr1-22、chrX，不含chrY） | 23条（不含chrY） | PASS | **CNV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特征。 **CNV染色体分布**：变异计数范围为20（chr22）至137（chrX），整体与染色体大小呈正比。chrX的变异计数（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。 # 数据集文件 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，大小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，大小48 MB 3. `15001711233855A.all_chroms.sv.pass.vcf.gz`：DELLY生成的合格结构变异文件，包含DEL、DUP、INV、BND、INS五类变异，大小845 KB 4. `15001711233855A.all_chroms.cnv.vcf.gz`：DELLY生成的读深度法CNV调用文件，包含合格与低质量变异，大小93 KB # 样本信息 - 受试者：Manuel Corpas（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 - 平均覆盖度：~30× - 测序平台：Illumina短读长测序技术 # 技术说明 - 参考基因组：GRCh37/hg19（UCSC），坐标采用1-based编号，每条染色体以chr前缀标识 - SNP/Indel调用：针对单样本场景，使用硬过滤替代VQSR流程 - 结构变异调用：DELLY基于双端读长与分裂读长证据进行识别，通过DELLY内置质量模型进行PASS过滤 - CNV调用：基于读深度分析，使用可映射性图谱进行GC校正，包含合格与低质量变异供用户自行筛选 - 计算资源与耗时：使用32核、256GB内存的Mac Studio完成分析，SNP/Indel分析耗时4小时19分钟，结构变异分析耗时51分钟，CNV分析耗时30分钟 # 知情同意与授权协议 本数据集由Manuel Corpas在完全知情同意的前提下自愿发布，用于个人基因组数据共享。本数据集基于CC0 1.0 通用公共领域贡献协议贡献至公共领域，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，数据提供者不对因使用本数据集产生的任何后果承担责任。 # 引用方式 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