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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AIBST-PGx Phenotypes

Whole-exome sequencing dataset for 127 individuals from 12 African populations (Kenya, Tanzania, Nigeria, South Africa, Zimbabwe). Library preparation used Agilent SureSelect 50 Mb capture; paired-end 76 bp sequencing on Illumina HiSeq2500 at 12x average depth. Reads aligned to GRCh38 with BWA-MEM2, duplicate-marked, base-quality recalibrated with GATK. Joint variant calling with DeepVariant v1.6 + GLnexus v1.4.1 in WES mode, with calling extended 2 kb beyond exome targets. Deposit: 127 per-sample CRAM files (GRCh38, recalibrated; LZMA-encoded, samtools 1.20; 224 GB total) plus one joint-called multi-sample VCF (~555 MB).

Request Access

DUO:0000006
version: 2021-02-23

health or medical or biomedical research

This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.

DUO:0000014
version: 2019-01-07

research use only

This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care).

DUO:0000018
version: 2021-02-23

not for profit, non commercial use only

This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.

DUO:0000019
version: 2021-02-23

publication required

This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.

DUO:0000019
version: 2019-01-07

publication required

This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.

DUO:0000024
version: 2021-02-23

publication moratorium

This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.

DUO:0000024
version: 2019-01-07

publication moratorium

This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.

DUO:0000027
version: 2021-02-23

project specific restriction

This data use modifier indicates that use is limited to use within an approved project.

DUO:0000027
version: 2019-01-07

project specific restriction

This data use modifier indicates that use is limited to use within an approved project.

DUO:0000042
version: 2019-01-07

general research use

This data use permission indicates that use is allowed for general research use for any research purpose.

H3ABioNet Data Submission Policy

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
EGAS00001008456 Other

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
EGAF00009063217 csv 11.2 kB
1 File (11.2 kB)