Submission

Submission flow

TogoVar-repository has two submission types SNP and SV.

• Short variants (SNP): variants ≤50 bp, exchanged with the NCBI dbSNP.
• Large structural variants (SV): variants >50 bp, exchanged with the NCBI dbVar.

BioProject and BioSample are necessary so that related data are grouped by BioProject and BioSample across databases. Metadata are prepared in the Excel format for each submission type. Variants are submitted in VCF. SV variant calls can also be submitted in the Excel sheet.

1. Create submission account

• Create a D-way submission account (Manual)
• Register a public key to your account to enable data upload to TogoVar-repository.

2. Apply submission

Apply your submission from the TogoVar-repository submission form. TogoVar-repository team will inform you how to submit your data.

3. Register BioProject

Register your project to BioProject. An accession number with prefix PRJDB will be assigned to your project.

4. Register BioSample

Register your samples to BioSample. Accession numbers with prefix SAMD will be assigned to samples.

5. Create metadata

Download a TogoVar-repository excel. The excel consists of the following sheets.

• TogoVar_Study: describes overall study.
• TogoVar_SampleSet: sample set (population).
• TogoVar_Sample: samples used.
• TogoVar_Experiment: experimental methods and analysis protocols.
• TogoVar_Dataset: dataset (1 dataset - 1 VCF).
• Variant Call (SV): when submitting variant calls in the sheet.
• Variant Region (SV): when submitting variant calls in the sheet.

6. Prepare data files

Provide variants (necessary), allele (recommended) and genotype (optional) frequencies in VCF. Please see the following VCF guidelines.

• dbSNP VCF Submission Format Guidelines
• dbVar VCF Submission Format Guidelines

7. Upload files

Upload a metadata Excel and VCF files to our file server by scp/sftp. Regarding how to upload your data files, please see “Data upload”.

Accession number

TogoVar-repository assigns accession numbers to objects with distinct prefixes. Please also see Overview of Structural Variation at dbVar.

• SNP/SV
  • study: dstd
• SNP
  • variant: dss
• SV
  • variant call: dssv
  • variant region: dsv

Data release

The data can remain private until your paper publication. Submitters can designate the hold date within three years and extend the date. The private data are released according to the data release policy.

Update

To update your data, please contact the TogoVar-repository team.