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SweGen whole-genome sequencing from the Northern Sweden Population Health Study

The dataset contains whole-genome sequencing data (aligned read files) in CRAM-format (lossless compression) 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
EGAF50000316303 crai 1.3 MB
Federated EGA
EGAF50000316304 crai 1.3 MB
Federated EGA
EGAF50000316305 crai 1.2 MB
Federated EGA
EGAF50000316307 crai 1.7 MB
Federated EGA
EGAF50000316308 crai 1.3 MB
Federated EGA
EGAF50000316309 crai 1.6 MB
Federated EGA
EGAF50000316310 cram 28.7 GB
Federated EGA
EGAF50000316311 crai 1.6 MB
Federated EGA
EGAF50000316312 cram 33.6 GB
Federated EGA
EGAF50000316313 crai 1.2 MB
Federated EGA
EGAF50000316314 cram 32.7 GB
Federated EGA
EGAF50000316315 crai 1.4 MB
Federated EGA
EGAF50000316316 cram 34.3 GB
Federated EGA
EGAF50000316317 crai 1.2 MB
Federated EGA
EGAF50000316318 cram 26.4 GB
Federated EGA
EGAF50000316319 crai 1.3 MB
Federated EGA
EGAF50000316320 cram 28.4 GB
Federated EGA
EGAF50000316321 crai 1.4 MB
Federated EGA
EGAF50000316322 cram 25.9 GB
Federated EGA
EGAF50000316323 crai 1.3 MB
Federated EGA
EGAF50000316324 cram 27.7 GB
Federated EGA
EGAF50000316325 crai 1.3 MB
Federated EGA
EGAF50000316326 cram 27.5 GB
Federated EGA
EGAF50000316327 crai 1.3 MB
Federated EGA
EGAF50000316328 cram 30.4 GB
Federated EGA
EGAF50000316329 crai 1.5 MB
Federated EGA
EGAF50000316330 cram 28.6 GB
Federated EGA
EGAF50000316331 crai 1.4 MB
Federated EGA
EGAF50000316332 cram 27.5 GB
Federated EGA
EGAF50000316333 crai 1.5 MB
Federated EGA
EGAF50000316334 cram 31.9 GB
Federated EGA
EGAF50000316335 crai 1.5 MB
Federated EGA
EGAF50000316336 cram 29.2 GB
Federated EGA
EGAF50000316337 crai 1.5 MB
Federated EGA
EGAF50000316338 cram 31.3 GB
Federated EGA
EGAF50000316339 crai 1.3 MB
Federated EGA
EGAF50000316340 cram 33.3 GB
Federated EGA
EGAF50000316341 crai 1.3 MB
Federated EGA
EGAF50000316342 cram 32.6 GB
Federated EGA
EGAF50000316343 crai 1.5 MB
Federated EGA
EGAF50000316344 cram 28.7 GB
Federated EGA
EGAF50000316345 crai 1.3 MB
Federated EGA
EGAF50000316346 cram 27.3 GB
Federated EGA
EGAF50000316347 crai 1.4 MB
Federated EGA
EGAF50000316348 cram 32.2 GB
Federated EGA
EGAF50000316349 crai 1.3 MB
Federated EGA
EGAF50000316350 cram 29.8 GB
Federated EGA
EGAF50000316351 crai 1.3 MB
Federated EGA
EGAF50000316352 cram 29.1 GB
Federated EGA
EGAF50000316353 crai 1.3 MB
Federated EGA
EGAF50000316354 cram 27.7 GB
Federated EGA
EGAF50000316355 crai 1.3 MB
Federated EGA
EGAF50000316356 cram 27.6 GB
Federated EGA
EGAF50000316357 crai 1.5 MB
Federated EGA
EGAF50000316358 cram 26.8 GB
Federated EGA
EGAF50000316359 crai 1.3 MB
Federated EGA
EGAF50000316360 cram 38.9 GB
Federated EGA
EGAF50000316361 crai 1.2 MB
Federated EGA
EGAF50000316362 cram 31.8 GB
Federated EGA
EGAF50000316363 crai 1.2 MB
Federated EGA
EGAF50000316364 cram 26.4 GB
Federated EGA
EGAF50000316365 crai 1.3 MB
Federated EGA
EGAF50000316366 cram 25.8 GB
Federated EGA
EGAF50000316367 cram 26.7 GB
Federated EGA
EGAF50000316368 crai 1.3 MB
Federated EGA
EGAF50000316369 cram 29.1 GB
Federated EGA
EGAF50000316370 crai 1.4 MB
Federated EGA
EGAF50000316371 cram 28.3 GB
Federated EGA
EGAF50000316372 crai 1.4 MB
Federated EGA
EGAF50000316373 cram 28.3 GB
Federated EGA
EGAF50000316374 crai 1.3 MB
Federated EGA
EGAF50000316375 cram 31.1 GB
Federated EGA
EGAF50000316376 crai 1.3 MB
Federated EGA
EGAF50000316377 cram 29.2 GB
Federated EGA
EGAF50000316378 crai 1.2 MB
Federated EGA
EGAF50000316379 cram 28.4 GB
Federated EGA
EGAF50000316380 crai 1.3 MB
Federated EGA
EGAF50000316381 cram 27.1 GB
Federated EGA
EGAF50000316382 crai 1.4 MB
Federated EGA
EGAF50000316383 cram 27.0 GB
Federated EGA
EGAF50000316384 crai 1.3 MB
Federated EGA
EGAF50000316385 cram 28.4 GB
Federated EGA
EGAF50000316386 cram 28.2 GB
Federated EGA
EGAF50000316387 crai 1.4 MB
Federated EGA
EGAF50000316388 cram 25.7 GB
Federated EGA
EGAF50000316389 crai 1.4 MB
Federated EGA
EGAF50000316390 cram 25.9 GB
Federated EGA
EGAF50000316391 crai 1.4 MB
Federated EGA
EGAF50000316392 cram 29.7 GB
Federated EGA
EGAF50000316393 cram 29.3 GB
Federated EGA
EGAF50000316394 crai 1.4 MB
Federated EGA
EGAF50000316395 cram 28.4 GB
Federated EGA
EGAF50000316396 crai 1.4 MB
Federated EGA
EGAF50000316397 cram 32.9 GB
Federated EGA
EGAF50000316398 crai 1.9 MB
Federated EGA
EGAF50000316399 cram 38.7 GB
Federated EGA
EGAF50000316400 crai 1.3 MB
Federated EGA
EGAF50000316401 cram 37.8 GB
Federated EGA
EGAF50000316402 crai 1.3 MB
Federated EGA
EGAF50000316403 cram 36.0 GB
Federated EGA
EGAF50000316404 crai 1.7 MB
Federated EGA
EGAF50000316405 cram 50.3 GB
Federated EGA
EGAF50000316406 crai 1.7 MB
Federated EGA
EGAF50000316407 cram 36.2 GB
Federated EGA
EGAF50000316408 crai 1.5 MB
Federated EGA
EGAF50000316409 cram 34.4 GB
Federated EGA
EGAF50000316410 crai 1.6 MB
Federated EGA
EGAF50000316411 cram 29.2 GB
Federated EGA
EGAF50000316412 crai 1.6 MB
Federated EGA
EGAF50000316413 cram 44.7 GB
Federated EGA
EGAF50000316414 crai 1.6 MB
Federated EGA
EGAF50000316415 cram 31.8 GB
Federated EGA
EGAF50000316416 crai 1.7 MB
Federated EGA
EGAF50000316431 cram 32.6 GB
Federated EGA
EGAF50000316534 cram 31.1 GB
Federated EGA
EGAF50000316535 cram 32.6 GB
Federated EGA
116 Files (1.8 TB)