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