About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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SweGen genetic variation from the Northern Sweden Population Health Study

The dataset contains files with single nucleotide variants in VCF format for a total of 58 DNA samples originating from the Northern Sweden Population Health Study (NSPHS). For each of the 58 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. The NSPHS study was approved by the local ethics committee at the University of Uppsala (Regionala Etikprövningsnämnden, Uppsala, 2005:325 and 2016-03-09). All participants gave their written informed consent to the study including the examination of environmental and genetic causes of disease in compliance with the Declaration of Helsinki.

Request Access

Uppsala University Data Access Policy

By depositing data in the FEGA repository, researchers at Uppsala University aims to contribute to science and advance discoveries in biomedicine, healthcare and other fields. Requests for access to data will be assessed based on Swedish laws and regulations, and are only accepted if data will be used for research. For requests from researchers outside the European Union, data will normally only be released to countries that the European Union considers to have an adequate level of data protection, see list of countries here: https://commission.europa.eu/law/law-topic/data-protection/international-dimension-data-protection/adequacy-decisions_en Requests must include information about the following aspects: - As genetic data is regarded as sensitive personal information, a request must describe how the data will be correctly handled in accordance to the laws and ethical guidelines in the receiving country. That should include an approval from an ethics committee or reference to national/equivalent guidelines. - Researchers in the European Union must specify the legal basis according to the General Data Protection Regulation (GDPR) to use the data. - Information on how data will be stored and handled in relation to the information security procedures at the receiving organization. Before data can be released the requester must be prepared to sign a “Warrant to respect” and a “Data Transfer Agreement” specifying the conditions that needs to be fulfilled for data to be released. Requesters need to be aware of that assessment of requests and preparation of agreements may be subject to lead times.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000000906 Whole Genome Sequencing

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50000316417 vcf.gz 222.2 MB
Federated EGA
EGAF50000316418 tbi 1.7 MB
Federated EGA
EGAF50000316419 vcf.gz 213.2 MB
Federated EGA
EGAF50000316420 tbi 1.7 MB
Federated EGA
EGAF50000316421 vcf.gz 216.8 MB
Federated EGA
EGAF50000316422 tbi 1.7 MB
Federated EGA
EGAF50000316423 vcf.gz 217.5 MB
Federated EGA
EGAF50000316424 tbi 1.7 MB
Federated EGA
EGAF50000316425 vcf.gz 209.7 MB
Federated EGA
EGAF50000316426 tbi 1.7 MB
Federated EGA
EGAF50000316427 vcf.gz 213.0 MB
Federated EGA
EGAF50000316428 tbi 1.7 MB
Federated EGA
EGAF50000316429 vcf.gz 208.3 MB
Federated EGA
EGAF50000316430 tbi 1.7 MB
Federated EGA
EGAF50000316432 tbi 1.7 MB
Federated EGA
EGAF50000316433 vcf.gz 211.7 MB
Federated EGA
EGAF50000316434 tbi 1.7 MB
Federated EGA
EGAF50000316435 vcf.gz 215.8 MB
Federated EGA
EGAF50000316436 tbi 1.7 MB
Federated EGA
EGAF50000316437 vcf.gz 212.7 MB
Federated EGA
EGAF50000316438 tbi 1.7 MB
Federated EGA
EGAF50000316439 vcf.gz 218.0 MB
Federated EGA
EGAF50000316440 tbi 1.7 MB
Federated EGA
EGAF50000316441 vcf.gz 211.2 MB
Federated EGA
EGAF50000316442 tbi 1.7 MB
Federated EGA
EGAF50000316443 vcf.gz 212.9 MB
Federated EGA
EGAF50000316444 tbi 1.7 MB
Federated EGA
EGAF50000316445 vcf.gz 211.2 MB
Federated EGA
EGAF50000316446 tbi 1.7 MB
Federated EGA
EGAF50000316447 vcf.gz 217.7 MB
Federated EGA
EGAF50000316448 tbi 1.7 MB
Federated EGA
EGAF50000316449 vcf.gz 218.2 MB
Federated EGA
EGAF50000316450 tbi 1.7 MB
Federated EGA
EGAF50000316451 vcf.gz 214.6 MB
Federated EGA
EGAF50000316452 tbi 1.7 MB
Federated EGA
EGAF50000316453 vcf.gz 217.4 MB
Federated EGA
EGAF50000316454 tbi 1.7 MB
Federated EGA
EGAF50000316455 vcf.gz 215.1 MB
Federated EGA
EGAF50000316456 tbi 1.7 MB
Federated EGA
EGAF50000316457 vcf.gz 216.8 MB
Federated EGA
EGAF50000316458 tbi 1.7 MB
Federated EGA
EGAF50000316459 vcf.gz 212.0 MB
Federated EGA
EGAF50000316460 tbi 1.7 MB
Federated EGA
EGAF50000316461 vcf.gz 212.2 MB
Federated EGA
EGAF50000316462 tbi 1.7 MB
Federated EGA
EGAF50000316463 vcf.gz 211.7 MB
Federated EGA
EGAF50000316464 tbi 1.7 MB
Federated EGA
EGAF50000316465 vcf.gz 211.3 MB
Federated EGA
EGAF50000316466 tbi 1.7 MB
Federated EGA
EGAF50000316467 vcf.gz 217.2 MB
Federated EGA
EGAF50000316468 tbi 1.7 MB
Federated EGA
EGAF50000316469 vcf.gz 207.4 MB
Federated EGA
EGAF50000316470 tbi 1.7 MB
Federated EGA
EGAF50000316471 vcf.gz 209.4 MB
Federated EGA
EGAF50000316472 tbi 1.7 MB
Federated EGA
EGAF50000316473 vcf.gz 213.2 MB
Federated EGA
EGAF50000316474 tbi 1.7 MB
Federated EGA
EGAF50000316475 vcf.gz 210.6 MB
Federated EGA
EGAF50000316476 tbi 1.7 MB
Federated EGA
EGAF50000316477 vcf.gz 215.1 MB
Federated EGA
EGAF50000316478 tbi 1.7 MB
Federated EGA
EGAF50000316479 vcf.gz 209.6 MB
Federated EGA
EGAF50000316480 tbi 1.7 MB
Federated EGA
EGAF50000316481 vcf.gz 214.5 MB
Federated EGA
EGAF50000316482 tbi 1.7 MB
Federated EGA
EGAF50000316483 vcf.gz 219.1 MB
Federated EGA
EGAF50000316484 tbi 1.7 MB
Federated EGA
EGAF50000316485 vcf.gz 216.9 MB
Federated EGA
EGAF50000316486 tbi 1.7 MB
Federated EGA
EGAF50000316487 vcf.gz 216.5 MB
Federated EGA
EGAF50000316488 tbi 1.7 MB
Federated EGA
EGAF50000316489 vcf.gz 212.2 MB
Federated EGA
EGAF50000316490 tbi 1.7 MB
Federated EGA
EGAF50000316491 vcf.gz 209.8 MB
Federated EGA
EGAF50000316492 tbi 1.7 MB
Federated EGA
EGAF50000316493 vcf.gz 211.2 MB
Federated EGA
EGAF50000316494 tbi 1.7 MB
Federated EGA
EGAF50000316495 vcf.gz 212.8 MB
Federated EGA
EGAF50000316496 tbi 1.7 MB
Federated EGA
EGAF50000316497 vcf.gz 215.8 MB
Federated EGA
EGAF50000316498 tbi 1.7 MB
Federated EGA
EGAF50000316499 vcf.gz 210.9 MB
Federated EGA
EGAF50000316500 tbi 1.7 MB
Federated EGA
EGAF50000316501 vcf.gz 215.9 MB
Federated EGA
EGAF50000316502 tbi 1.7 MB
Federated EGA
EGAF50000316503 vcf.gz 215.0 MB
Federated EGA
EGAF50000316504 tbi 1.7 MB
Federated EGA
EGAF50000316505 vcf.gz 203.5 MB
Federated EGA
EGAF50000316506 tbi 1.7 MB
Federated EGA
EGAF50000316507 vcf.gz 202.2 MB
Federated EGA
EGAF50000316508 vcf.gz 207.2 MB
Federated EGA
EGAF50000316509 tbi 1.7 MB
Federated EGA
EGAF50000316510 tbi 1.7 MB
Federated EGA
EGAF50000316511 vcf.gz 222.6 MB
Federated EGA
EGAF50000316512 tbi 1.7 MB
Federated EGA
EGAF50000316513 vcf.gz 222.3 MB
Federated EGA
EGAF50000316514 tbi 1.7 MB
Federated EGA
EGAF50000316515 vcf.gz 218.0 MB
Federated EGA
EGAF50000316516 tbi 1.7 MB
Federated EGA
EGAF50000316517 vcf.gz 224.2 MB
Federated EGA
EGAF50000316518 tbi 1.7 MB
Federated EGA
EGAF50000316520 tbi 1.7 MB
Federated EGA
EGAF50000316521 vcf.gz 220.9 MB
Federated EGA
EGAF50000316522 tbi 1.7 MB
Federated EGA
EGAF50000316523 vcf.gz 211.2 MB
Federated EGA
EGAF50000316524 tbi 1.7 MB
Federated EGA
EGAF50000316525 vcf.gz 215.5 MB
Federated EGA
EGAF50000316526 tbi 1.6 MB
Federated EGA
EGAF50000316527 vcf.gz 193.8 MB
Federated EGA
EGAF50000316528 tbi 1.7 MB
Federated EGA
EGAF50000316529 vcf.gz 198.1 MB
Federated EGA
EGAF50000316530 tbi 1.7 MB
Federated EGA
EGAF50000316531 vcf.gz 202.8 MB
Federated EGA
EGAF50000316532 tbi 1.7 MB
Federated EGA
EGAF50000316533 vcf.gz 202.4 MB
Federated EGA
115 Files (12.2 GB)