The principal investigator (PI) of the project or downloaders designated by the PI can download the data as soon as the data access request (DAR) is approved. The recommended way of downloading dbGaP data is to use the “prefetch” utility available in the NCBI SRA toolkit.

The prefetch utility can download dbGaP non-SRA and SRA data files in bulk when a cart file is provided as an argument. It can also download the data of an individual SRA run when an individual SRR accession is provided as an argument. Please refer to the SRA dbGaP Download Guide for detailed instructions.

Principal investigators (PIs) may designate one or more Downloaders within the PI's institution from inside the Authorized Access Portal. A Downloader is an individual assigned by the PI to perform the time-consuming task of retrieving large data files. Downloaders can login to dbGaP through their own account. The download is limited to the datasets approved for the Downloader by the primary PI.

Most of the sequencing data available through dbGaP are in SRA format. SRA can be converted to BAM using the sam-dump utility in the SRA toolkit.

Please visit the section related to the fasterq-dump utility in the SRA Toolkit guide.

DbGaP phenotype, genotype, and sequencing data (including BAM, SRA, etc.) may be submitted and processed separately. As a consequence, the IDs used in different data files may be in different naming formats.

1. Phenotype subject and sample ID mapping
   The master mapping files between subject and sample IDs can be found from the files that have the string “_Subject”, “_Sample”, or “_Pedigree” embedded in the file name. For example:
   • phs000094.v1.pht000000.v1.p1.Oral_Clefts_Subject.MULTI.txt
   • phs000094.v1.pht000000.v1.p1.Oral_Clefts_Sample.MULTI.txt
   • phs000094.v1.pht000000.v1.p1.Oral_Clefts_Pedigree.MULTI.txt


2. Genotype ID mapping
   The sample and subject ID mapping information for genotype files can be found in a file packed in the tarball that has the phrase “sample-info” embedded in the file name. For example:
   • phg000054.v1.p1.GENEVA_OralClefts.sample-info.MULTI.tar
   Please note that the IDs in the sample-info file may not be exactly identical to those used in the master mapping files mentioned above.
   


3. SRA sample ID mapping
   SRA samples are given independent IDs at different stages of data processing, handling, and archiving. Most of the SRA samples distributed through dbGaP have submitted_sample_id, sra_accession, sra_sample_id, and dbgap_sample_id. The “Dataset Manifest” file contains SRA sample ID mapping.

1. SUBJID
   The SUBJID is the submitted subject ID and is included in the Subject Consent Data File, Subject Sample Mapping Data File, Pedigree Data File (if available), and all Subject Phenotype Data Files. A Subject is defined as a single human individual that arises from a single germline. In addition to the submitted Subject ID, dbGaP will assign a dbGaP Subject ID that will be included in the final phenotype dump files along with the submitted Subject ID.
   
   
2. dbGaP SubjID
   The dbGaP Subject ID is included as a column in the final phenotype dump files whenever there is a submitted subject ID column. The dbGaP Subject ID is unique across all dbGaP studies, which means that if a subject is known to have participated in multiple studies that have been submitted to dbGaP, the same dbGaP SubjID will be assigned to the individual across multiple studies, even when the submitted subject ID may be different.
   
   
3. SAMPID
   The SAMPID is the submitted sample ID and is included in the Subject Sample Mapping Data File and Sample Attributes Data File. A dbGaP Sample is defined as the final sample preparation. A single subject can have multiple samples. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate two sequencing runs or one sequencing run and one genotyping array, there would be two rows, both using the same subject ID, but having two unique sample IDs. The SAMPIDs listed in the Subject Sample Mapping Data File should be identical to the sample IDs found in the genotype and SRA Data. In addition to the submitted Sample ID, dbGaP will assign a dbGaP Sample ID that will be included in the final phenotype dump files along with the submitted Sample ID.
   
   
4. dbGaP SampID
   The dbGaP Sample ID is a dbGaP assigned identifier that is included as a column in the final phenotype dump files whenever there is a submitted sample ID column.
   
   
5. SOURCE_SUBJID and SUBJ_SOURCE
   For subjects originating from a shared source (such as a public repository, consortium, institute, study, etc.) or for subjects with alias IDs, SOURCE_SUBJID and SUBJ_SOURCE will be included in the Subject Consent Data File. The Subject Source (SUBJ_SOURCE) is the name of the third party, public repository, consortium, institute, or study that corresponds to the subject. The Source Subject ID (SOURCE_SUBJID) is the de-identified alias Subject ID used in the public repository, consortium, institute, or study from where the subject has been obtained. The SOURCE_SUBJID maps to the SUBJID. For referencing HapMap subjects from Coriell, the SUBJ_SOURCE value is written as “Coriell.” The SOURCE_SUBJID should be written as the de-identified subject ID assigned by Coriell.
   
   
6. SEX
   The SEX variable can be included in a subject phenotype data file or in a pedigree file if a pedigree file is available.
   
   
7. FAMID
   The family ID (FAMID), also called the Pedigree ID, is found in the pedigree file if a pedigree file is available. FAMID is de-identified and should be the same for individuals belonging in the same biological family.
   
   
8. FATHER and MOTHER
   Every individual father has a unique, de-identified FATHER ID; every individual mother has a unique, de-identified MOTHER ID. This ID will be reported as 0 (zero) or blank for founders or marry-ins (parents not specified) in a pedigree. Each unique FATHER ID and unique MOTHER ID is also listed in the SUBJID column of both the Pedigree Data File and the Subject Consent Data File.
   
   
9. CONSENT
   Every subject that appears in a Subject Phenotype Data File must belong to a consent group (to allow their phenotypes to be used by approved Authorized Access users) and every sample that appears in a Sample Attribute Data File must belong to a consented subject. The consent information is listed in the Subject Consent Data File. Each subject can only belong to a single consent group. The consents are determined by the submitter, their IRB, and their GPA (Genome Program Administrator). All data is parsed into its respective consent groups for download.