Personal Whole Genome Sequencing Variant Calls (SNPs and Indels) 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. 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). Variant Calling Pipeline Variant discovery followed the GATK Best Practices workflow (GATK v4, Broad Institute): HaplotypeCaller: Per-chromosome GVCF generation in ERC mode, parallelised across 24 chromosomes (chr1-22, chrX, chrY) on a 32-core Apple Mac Studio with 256 GB RAM. CombineGVCFs: Merged per-chromosome GVCFs into a single multi-chromosome GVCF. GenotypeGVCFs: Joint genotyping across all chromosomes. Hard Filtering (GATK Best Practices thresholds for single-sample calling):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 Output: Two compressed VCF v4.2 files containing only high-confidence PASS variants. Dataset Statistics MetricSNP VCFIndel VCFTotal PASS variants3,716,648912,009Multiallelic sites8,83686,033Chromosomeschr1-22, chrX, chrYchr1-22, chrX, chrYCompressed file size166 MB48 MBMD5 checksum72b728aefe54f9492b108c23ca7539bf0e173b22b24eb98b2193029ae65a2a8f The total of 4,628,657 variants (3.72M SNPs + 912K indels) is consistent with expected values for a 30x WGS of a Southern European individual. Quality Control Report All QC metrics fall within published reference ranges for 30x Illumina WGS of a European individual. 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 errors0PASSPipeline errors00PASSMin QUAL score30.0≥30PASS Ti/Tv Ratio: The transition/transversion ratio of 2.03 is the most important single QC metric for SNP calling quality. Values outside the 2.0-2.1 range for whole genome data indicate systematic variant calling errors. The observed value of 2.03 confirms high-quality, unbiased SNP discovery. Het/Hom Ratio: The heterozygous-to-homozygous ratio of 1.63 is consistent with a Southern European individual from an outbred population. Deviation from the 1.5-2.0 range would suggest contamination, consanguinity, or technical artefacts. Genotype Distribution (SNPs): 62% heterozygous (0/1), 38% homozygous alternative (1/1). Physical phasing information is present for a subset of variants (0|1 genotypes). Per-Chromosome Variant Counts (SNPs): chr1: 282,227; chr2: 304,055; chr3: 250,531; chr4: 267,108; chr5: 222,447; chr6: 223,795; chr7: 215,352; chr8: 190,617; chr9: 158,539; chr10: 186,546; chr11: 186,962; chr12: 171,631; chr13: 139,155; chr14: 119,333; chr15: 107,806; chr16: 119,293; chr17: 99,040; chr18: 106,225; chr19: 85,092; chr20: 84,920; chr21: 60,515; chr22: 49,832; chrX: 73,494; chrY: 12,133. Counts scale proportionally with chromosome size. chrY count of 12,133 is consistent with a male sample. Indel Size Distribution: Classic L-shaped distribution peaking at single-base insertions (+1 bp: 229,139) and deletions (-1 bp: 235,557), declining with increasing indel size. This pattern is consistent with known biological properties of germline indel mutagenesis in the human genome. Validation: Both VCF files passed GATK ValidateVariants with zero errors against the hg19 reference. All 24 HaplotypeCaller jobs completed with exit code 0. No errors were found in any pipeline log file. MD5 checksums were verified at upload. Files 15001711233855A.all_chroms.snp.vcf.gz - Hard-filtered PASS SNP calls, all chromosomes (VCF v4.2, bgzipped, 166 MB) 15001711233855A.all_chroms.indel.vcf.gz - Hard-filtered PASS indel calls, all chromosomes (VCF v4.2, bgzipped, 48 MB) 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 (chr1, chr2, etc.). Hard filtering was used instead of VQSR because VQSR requires a multi-sample cohort for reliable recalibration. The hard filter thresholds applied follow GATK Best Practices recommendations for single-sample germline calling. VCF annotations include: allelic depth (AD), read depth (DP), genotype quality (GQ), phred-scaled likelihoods (PL), and physical phasing information (PGT/PID) where available. Users wishing to lift over to GRCh38 should use the UCSC liftOver tool or Picard LiftoverVcf with the hg19-to-hg38 chain file. Processing time: 4 hours 19 minutes on a 32-core Apple Mac Studio (M-series, 256 GB RAM), with HaplotypeCaller parallelised across 24 chromosomes. 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 direct, indirect, incidental, or consequential damages arising from the use of this data. This release is made in the spirit of open science and the belief that personal genomics data sharing accelerates research for the benefit of all. Citation If you use this dataset, please cite: Corpas, M. (2026). Personal Whole Genome Sequencing Variant Calls (SNPs and Indels) of Manuel Corpas from Dante Labs 30x WGS. Zenodo. https://doi.org/10.5281/zenodo.19285821