How to Submit to dbSNP:
VI. Formatting Data for Submission
Version 4.1; December 11, 2015
dbSNP only accepts variant data submissions in VCF, or Variant Call Format. Please note that dbSNP does not accept any variant data submitted in Flat File format.
VCF Submission Format
There are two steps for formatting a dbSNP VCF submission:
-
Create the required metadata (i.e. metafiles) for the publication, method, population, and assay information associated with the submission.
a. Specifications for each Meta file are available in the Metafile Specification section of the Formatting Metadata (Meta)files document.
b. You can submit these Meta files separately or combine them into a single text file for submission. -
Create a VCF Submission file for your data using the detailed instructions in the dbSNP VCF Submission Format Guidelines, or if you have a small submission or intend to input data by hand, use the VCF Excel template to format your submission. Your VCF submission file should include:
a. a properly formatted dbSNP VCF file header
b. a data table that contains the required INFO tags for the variants you are submitting
c. optional INFO tags that describe your data more fully. - Validate your VCF file using the dbSNP VCF Online Validator.
Once you have completed your VCF submission data file and wish to send your data to dbSNP, use the instructions in the Submission Quick Start document.
Excel Flat File Submission Template
IMPORTANT: dbSNP does not accept variant data submissions in Flat File format using our Excel flat file submission template.
Data Submission Options
Submitting Variations without Genotype and Frequency Data
Submitting genotype and frequency data to dbSNP is optional. You can submit a variant to dbSNP without genotype or frequency data in VCF format. Fill out the VCF submission template without using the optional INFO tags for frequency and genotype.
Submitting Genotypic or Allele Frequency Data for Existing Variants in dbSNP
You can submit genotypic data for existing variants in dbSNP using the VCF format:
- VCF: Submit genotype data for existing variations using the dbSNP’s VCF Submission template. Follow the genotype submission example provided by 1000 Genome Project in their description of VCF version 4.1.
- IMPORTANT: Beginning November 1, 2017, dbSNP will no longer accept genotype frequency and allele frequency information for existing variants in SNPPOPUSE format, located at “templates_SNPsub.xls”, in the submission file of the /specs subdirectory of the dbSNP FTP site.
Contact dbSNP
If you do not find the answer to your submission questions in the How to Submit to dbSNP document series, contact dbSNP submissions at [email protected], and we will do our best to answer your submission question or help you solve a difficult submission problem.
- Send submissions and submission questions to: [email protected]
- Send submission updates to: [email protected]
- Send general inquiries, etc. to: [email protected]
Titles in the How to Submit to dbSNP Series: