dbVar Submission Guidelines

   NOTE TO SUBMITTERS:

  • Beginning September 1, 2017,  NCBI will no longer accept submissions of non-human organisms data. You can submit your data to European Variation Archive (http://www.ebi.ac.uk/eva/), one of our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Additional details related to this change are available on NCBI Insights (https://go.usa.gov/x5MUQ). 
  • If your data include clinical assertions, STOP! Variants with clinical assertions must be submitted to ClinVar, not dbVar. Clinical information will be stored in ClinVar, and structural variants will automatically be forwarded to dbVar. See the ClinVar submission page for more information.
  • If your data include sensitive clinical information or personally identifying information, STOP! Variants fitting this description must be submitted to dbGaP, not dbVar. dbGaP will store the necessary information behind controlled access, and forward anonymized aggregate structural variants to dbVar. SeedbGaP for more information.
  • Submit your data early. To avoid last-minute delays in the publication process, submit your data to dbVar well in advance so we have time to prepare it for access by journal editors. If you indicate a hold date in your submisson, we will not release your data before the date you indicate.

This page provides instructions and tips to help you navigate the submission process. dbVar accepts data in Excel, Tab-delimited textXML, and VCF formats – submission templates can be downloaded here. Most submitters use Excel or VCF; the Excel template contains instructions and other helpful information that are not present in the other templates – therefore you may find it helpful to refer to the Excel template regardless of the format in which you submit.

Before preparing your submission

  • (Required – exceptions noted below)  dbVar prefers that all variant asserted positions are submitted on a sequence accession that is part of an assembly housed in the NCBI Assembly Resource.
    • NOTE 1: SV submitted with positions on a sequence that is part of an assembly housed in the NCBI Assembly Resource will be remapped to the latest assembly version and distributed as part of the dbVar monthly build release cycle. This allows the reported variation to appear on maps or graphic representations of the assembly, and to be integrated with NCBI's other resources like Variation Viewer, Variation Reporter, Gene, ClinVar, dbGAP and PubMed.
    • NOTE 2: SV submitted with positions on a sequence that does not yet align to an assembly in NCBI's Assembly Resource – either because there is not yet an assembly to which the sequence aligns, or because the submitted sequence aligns to a gap in an existing assembly – will include only the asserted locations that were submitted. The reported variation will NOT appear on maps or graphic representations of the assembly, and it will NOT be integrated with NCBI's other resources. The SV with asserted locations will still be available for download on our FTP site. If at some future date a new assembly is created, or an old assembly is updated, such that the reported variant sequence aligns to an assembly in the NCBI Assembly Resource, then the reported SV will automatically be remapped and distributed as part of the regular dbVar release cycle.
  • Deposit your raw data in a public database. If you have not already done so, deposit all sequence and/or array data in a public database - e.g., GenBank, GEO, dbGaP, SRA or Trace.
  • Clinical assertions go to ClinVar and sensitive clinical information goes to dbGaP. As mentioned in the banner at the top of this page: If your data contain clinical assertions, they cannot be submitted directly to dbVar – they must first go to ClinVar. Similarly, if your data contain sensitive clinical information, or if the individuals in whom the variants were observed have not consented to the display of their genetic information on a free public website, you must submit your study to NCBI's Database of Genotypes and Phenotypes (dbGaP). Sensitive information will be stored behind controlled access at dbGaP while aggregate data, stripped of personally identifying information, will be forwarded to dbVar. NOTE: When submitting structural variation data to dbGaP, you must still use the VARIANT CALLS section of the dbVar submission template to define your variants – the dbVar template captures details of structural variation that are not captured in the dbGaP template. ClinVar's submission template does accommodate structural variants and cab be used independently of the dbVar submission template.
  • Get a MyNCBI ID (strongly encouraged). If you do not already have a MyNCBI login please create one here. Your MyNCBI ID** will be used to track your study at NCBI, and is very useful to help integrate your study data with numerous other resources at NCBI.
  • Get a BioProject accession (strongly encouraged). NIH-funded projects should be registered in BioProject with the assigned BioProject accession associated with the grant number for compliance with NIH Genomic Data Sharing (GDS) Policy (http://gds.nih.gov/). If your data is not already associated with an NCBI BioProject accession, please request one via the NCBI Submission Portal. You will need a BioProject accession when you complete the STUDY tab of the dbVar submission template. Your accession will further facilitate dbVar's ability to track your data and to integrate them across a variety of NCBI resources.

Hold data until publication

If you want dbVar to withhold public release of your data (for example to coincide with the publication of a manuscript), indicate your request using the hold_date field in the Study section of the template. Simply enter the date after which we may share your data with the public. You may change or remove the hold date at any time by contacting dbVar.

Genotype Data

Genotype data are stored separately from dbVar, in NCBI's Genotype Server. If you are submitting genotype data, use the VCF submission format. More information can be found in the dbVar VCF specification.

Submitting your data to dbVar

Step One -

Choose a format for your submission - Excel, Tab-delimited text, XML, or VCF - and download the appropriate pre-defined template here. Details specific to individual template formats can be found here: Excel, Tab-delimited, XML, VCF. Complete details and submission instructions are found only in the Excel template, so use it as a reference regardless of the format in which you submit.

Step Two -

Use the Help sections in the Excel atemplates your primary guide, whether your submission is in Excel or a different format. You may also refer to other documentation found on this web site. If you need assistance, email us at dbvar@ncbi.nlm.nih.gov.

Step Three -

Email your submission to dbvar@ncbi.nlm.nih.gov. You will receive a response confirming receipt of your submission within 24 hours. If confirmation does not arrive, contact us by email or notify the NIH Help Desk. dbVar publicly releases new data on a monthly schedule. Barring any delays in processing, your data should be available on the public dbVar site three to six weeks from the date of submission (often sooner).

Thank you for submitting your structural variation data to dbVar!

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Last updated: 2017-11-13T12:49:57Z