Genome of Switzerland (GoS) Pilot: Aggregated Allele Counts of Small Variants from 1000 Whole Genomes

Summary This record contains aggregated allele counts of small variants (SNVs and short indels) called from whole-genome sequencing (WGS) data of 1000 individuals in the pilot phase of the Genome of Switzerland (GoS) project. It is intended as a population reference resource and provides no individual-level genotypes. File formatThe data are provided as a single gzip-compressed, tab-separated file (.tsv.gz) with a header line and one row per variant, with the following columns: Column Description CHR Chromosome (with "chr" prefix, e.g. chr1) POS Position on GRCh38 (1-based) of the first reference base REF Reference allele ALT Alternate allele AN Total number of confident allele calls at this site (allele number) AC Number of alternate alleles observed (allele count) AC_hom Number of individuals homozygous for the alternate allele Usage notes AC and AN count alleles, whereas AC_hom counts individuals. AN can be lower than 2 × 1000 since some individuals have no confident genotype call at a certain site, for example because of low coverage or low mappability in repetitive regions. Because no additional quality filtering was applied (e.g. on quality, depth, genotype quality, or site-level filters), the counts might include lower-confidence artifacts. This is a pilot dataset with a limited sample size. Rare-variant frequencies may be imprecise and may not be representative of the whole Swiss population. Data production and processing Samples underwent whole-genome sequencing (WGS) with Illumina short-read technology at approximately 30x mean coverage. Reads were processed per sample with the Illumina DRAGEN platform, version 4.3.13 (alignment and small-variant calling, producing gVCFs) using GCA_000001405.15_GRCh38_no_alt_analysis_set as a reference genome. Per-sample gVCFs were combined using the DRAGEN iterative gVCF genotyper (iGG), and allele counts were aggregated from the resulting joint VCF. No additional quality filtering was applied. Only autosomes (chr1-chr22) are included; sex chromosomes and the mitochondrial genome are not. Multiallelic sites were split into separate rows. Samples, ethics and consentSamples were obtained from the Lausanne University Hospital (CHUV) Genomic Biobank (BGC), where all participants provided general consent for the use of their coded health-related data and samples for research. BGC operations are approved by the Ethics Committee of the Canton of Vaud (CER-VD; reference 144/12). Related dataThis record contains aggregated allele counts only. The GoS Pilot dataset in FASTQ and VCF format is registered in the Swiss Personalized Health Network (SPHN) Metadata Catalogue: SPHN FAIR Data Point entry https://fdp.dcc.sib.swiss/catalog/087d497a-6f23-564d-a77a-a989a4df5d67. FundingThe project was funded by the ETH Focus Area Personalized Health and Related Technologies (PHRT) and the Swiss Personalized Health Network (SPHN).