The genome browser contains data about the genomic location, frequencies, and functional consequences of genetic variants for 30,703,820 variants in 9,425 individuals in the Slovenian population.
The data for the browser was generated using analytical pipelines that are based on recommendations for good genomic practice (GATK best practice guidelines), utilizing modified WDL workflows in the Warp repository of the Broad Institute (https://broadinstitute.github.io/warp/).
To obtain the information on genetic variability in the population, data from exome and genome sequencing was initially aligned to the reference genome hg38, and primary variant detection was performed (WholeGenomeGermlineSingleSample.wdl). The obtained GVCF files were used for variant detection in a cohort mode (JointGenotypingImport.wdl and JointGenotypingGenotype.wdl), providing data on variant frequencies within the Slovenian population.
The NGS data of 9,425 individuals originates from whole genome (619 individuals) and whole exome sequencing (8,806 individuals) using Illumina platform. Both datasets were first analyzed separately, and the obtained results were then combined into a unified set of variants. All reported pathogenic variants were subsequently removed and frequencies were adjusted to reflect their occurrence in the population of healthy Slovenians.
Within the present browser, we retained single nucleotide variants (SNPs) and short insertion-deletion variants (indels) with a detection quality (QUAL) above 100.0 and genotypes with a quality (GQ) above 20.0. The browser displays anonymized and aggregated data of the frequencies of detected variants within the Slovenian population. An API access (Bravo API help) is enabled to submit queries programmatically and to obtain data as JSON objects.
The analyses were conducted using the SLING network and primarily with the capacities of the supercomputer Vega. We sincerely thank the collaborators at the Jožef Stefan Institute for their invaluable support in utilizing the capacities of the Slovenian supercomputing network. We also extend our gratitude to the ARNES network for enabling the hosting of the browser. Finally, we acknowledge NHLBI's TOPMed program for the open-coded development of the Bravo variant server.
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