Data submission
Phasing out support for the Database of Genomic Variants archive (DGVa).
The submission, archiving, and presentation of structural variation services offered by the DGVa is transitioning to the European Variation Archive (EVA). All of the data shown in the DGVa website is already searchable and browsable from the EVA Study Browser.
Submission of structural variation data to EVA is done using the VCF format. The VCF specification allows representing multiple types of structural variants such as insertions, deletions, duplications and copy-number variants. Other features such as symbolic alleles, breakends, confidence intervals etc., support more complex events, such as translocations at an imprecise position.
We expect to cease accepting direct submissions to DGVa at the end of 2019, in the meantime we recommend submitters make SV submissions to the EVA. If there are specific difficulties with preparing SV submissions in VCF format, please contact the EVA helpdesk.
Submitting to DGVa
Genomic structural variation can be complex to represent. We strongly urge submitters to take the 'DGVa Quick tour' by clicking the link on the menu to the left of this screen. This is a guided tour of DGVa and takes less than 30 minutes to complete; understanding the DGVa and how data is stored will greatly assist in the completion of submission files.
In addition to structural variation data we also require information about the study, including details of the subjects/samples, experimental protocols and applied analyses. Data can be submitted in a number of formats, and public release can be delayed if required (e.g. until after your manuscript has been published.)
Before submitting
If your study has generated raw sequence or aCGH data, this should be deposited in a public database, such as the European Nucleotide Archive (ENA) or ArrayExpress at EBI - the DGVa accepts processed structural variant data only.
Submitting your data
Choose a format for your submission
The DGVa accepts submission data as an Excel spreadsheet and/or tab-delimited text files. Whichever format you choose, please download and use the Submission template as a reference, as it shows which information is required and which is optional.
Complete your submission spreadsheet/files
The DGVa has a fairly well-defined criteria for the type of information that can be entered. However, if you would like to add extra information, or need additional guidance, please email the DGVa helpdesk at [email protected].
Send your submission files to DGVa
Email the submission file(s) to [email protected], receipt of which will be confirmed by email. Please email the DGVa helpdesk at [email protected] if you wish to submit via ftp.
What happens next?
Validation
Your submission files will be validated to ensure they provide the required information, in the correct format. You will be notified by email if amendments are requested.
Accessioning
After data has been loaded to the archive, unique and stable accession numbers will be assigned for the study, variant regions, and all sample level variants (variant calls.)
Public Release
The study dataset becomes available for download at our data download page. Data are also automatically integrated with other EBI resources, can be graphically viewed in the genomic context using the Ensembl genome browser, or queried and retrieved using Ensembl Biomart. You will be notified by email when this takes place.