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 Agreement

Uppsala University FEGA Access guide Requests for data Requests for access to these data will be assessed based on Swedish laws and regulations. Requests must include an explicit acceptance of the conditions stated below and information about the following aspects: - The requester must attach an approval from an ethics committee or equivalent body that allows the data to be handled in accordance to the laws and ethical guidelines in the receiving country. - For researchers in the European Union – specify the legal basis according to GDPR to use the data. - Information about how the data will be stored and managed with regards to information security procedures. Requests for data are only accepted if the recipient adheres to the following conditions: Purpose - The recipient agrees to use data only for research. Confidentiality -The recipient agrees to preserve, at all times, the confidentiality of data pertaining to identifiable data subjects. Data protection - Recipients in EU agrees that it, and its registered users, are covered by and shall comply with the obligations contained in the General Data Protection Regulation (EU) 2016/679 ("GDPR"). Upon receipt of the data, the recipient will become controller of the personal data as defined in the GDPR. Recipients outside EU shall comply with relevant national laws concerning the protection of personal data. Uppsala University reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures. The recipient agrees that it, and its registered users, shall not analyse or make any use of the data in such a way that has the potential to: (a) lead to the identification of any data subject; or (b) compromise the protected identity of any data subject in any way. Access and Governance - The recipient agrees that it shall take all reasonable security precautions to keep the data confidential. The recipient agrees to, under no circumstances, give access to data to any third party, except to registered users (as described below). The recipient agrees to only give access to data, in whole or part, or any identifiable material derived from the data, to a registered user. The recipient agrees that before it gives any registered user access to data, it shall first inform about the conditions stated in this text and that he or she must comply with the obligations. The recipient shall only give registered users that are not researchers (including but not limited to students or new researchers to the field) access to the data if they are supervised by a researcher who will take responsibility for such registered users’ use of the data. The recipient must make sure that: - Data is processed in a way that ensures the confidentiality and integrity of the data. - Analysis and storage of the data must be performed in a secure environment that ensures that only registered users have access to the data. - Transfer of data must be done through encrypted channels. - There are standard operating routines that ensure that registered users handle the data in accordance with information security and legal requirements. - In the case of a personal data breach, the recipient must immediately inform Uppsala University, and the appropriate national data protection authority, of such an incident. Errors - The recipient must notify the Uppsala University of any errors detected in the data. Acknowledgement of data use - The recipient agrees to acknowledge the creators and source of the data in any work based in whole or part on the Data. Definitions: “Research” shall mean research that is seeking to advance the understanding of the research purpose stated in the ethics approval or equivalent document. “Registered User” shall mean a researcher (or an individual conducting research under the supervision of a researcher) that is employed by the recipient and is bound by confidentiality and has been informed of the conditions stated above. For the avoidance of doubt, “Registered User” may also include students, visiting academics, contractors, sub-contractors or independent consultants provided that any such individual is bound by confidentiality and non-use obligations no less onerous than those binding the recipient’s employees.

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
EGAF50000316519 vcf.gz 221.1 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
116 Files (12.5 GB)