European Variation Archive

The European Variation Archive (EVA) is EMBL-EBI's open-access genetic variation archive. The EVA accepts submission of all types of precise genetic variants, ranging from single nucleotide polymorphisms to large structural variants, observed in germline or somatic sources, from any organism. The EVA permits access to these data at two distinct levels:

i) The raw variant data as was submitted to the EVA, via the EVA Study Browser

ii) The normalised and processed variant data, via the EVA Variant Browser and EVA API

dbSNP and dbVar

Database of Genomic Variants Archive

Europe PubMed Central

Open Targets

Accelerating Medicines Partnership - Type 2 Diabetes

European Nucleotide Archive and Biosamples

Ensembl

Global Alliance for Genomics and Health

Elixir

The following are our GitHub repositories:

Acknowledgement

We would like to acknowledge the following software support.

Links are shown on the EVA Study Browser to both the raw submitted files and the 'EVA browsable files'. Not all submitted VCF files for a study are browsable due to overlapping information. For example, we have studies where the submitted VCF files contain the sample and variant data split by population, but also merged together. It would be redundant for the EVA to load all of these data to our variant warehouse. Please note that due to processing time required not all studies have 'EVA browsable files' just yet.

Additionally users can download query results from the EVA variant browser directly and all of our loaded data is available programmatically via our API.

The EVA website employs HTML5 technologies and standards and is optimized for use with modern browsers. In particular, Chrome (version 73 or higher) and Firefox (version 66 or higher) are fully supported, however older versions of these browsers may give rise to errors.
The EVA website also supports mobile versions of web browsers, with limited functionality. Please report all errors to the EVA helpdesk.

The EVA offers users the ability to search both the EVA Variant Browser and API using existing dbSNP 'SS' and 'RS' identifiers, as well as those that are newly generated by the EVA.

Yes. After an rs build the EVA will provide a VCF dump for each species/assembly combination. These files shall be in the same style as the current VCFs that dbSNP generates (i.e. contain the rs ID positional information, but not the genotypic nor annotation data). Furthermore we are developing a 'VCF Dumper' tool which shall allow users to generate a custom VCF file based on filtering options available at the EVA Variant Browser.

In addition to outputting a VCF file for each rs build the EVA shall also generate a file that will allow users to track changes to variant numbers over time. These files shall include details of all newly generated identifiers for each rs build, a list of those variants that have been deprecated as well as information on any variants that have been merged together. The EVA shall follow the same rules as dbSNP for generating, deprecating and merging variant identifiers.

The EVA provides to the community a completely free, secure and permanent solution to data sharing. Each project, VCF file and sample that is submitted to the EVA is assigned a unique identifier that is accessible in perpetuity and is therefore able to be referenced in publication, for example. The EVA helpdesk provides support to submitters, and users, to ensure accurate represention and proper integration of the submitted data with other EMBL-EBI resources such as the EGA and Ensembl. A final advantage of submitting to the EVA is that variants are brokered to the National Centre for Biotechnology Information (NCBI) on the submitter's behalf, negating the requirement for independent submissions.

The most important consideration is that all data archived at the EVA is open access. As such, there are no restrictions as to who can access the data or how such data is reused. It is the submitter's responsibility to ensure that the data archived at the EVA complies to this open access policy.
If consent was gathered for any individual genotype data in the study then we will require a consent statement to be completed prior to submission.

Genetic variants submitted to the EVA must be described in the Variant Call Format (VCF). The EVA only accepts VCF files that adhere to the specification and match a reference sequence (Versions v4.1, v4.2, & v4.3 accepted) Submitters can make use of the EVA VCF validation suite to ensure they fulfill these requirements. Furthermore, VCF files submitted to the EVA should provide either sample genotypes and/or aggregated sample summary-level allele frequencies. Variant lines should also be unique and not specify duplicate loci as this causes issues during steps such as calculation of population frequencies. Although both per-sample VCFs and merged VCFs are acceptable, merged VCF files containing sample information through the FORMAT field are preferred over separate VCF files for each sample. Single VCF files allow data to be easily reusable and reproducible. Therefore, we recommend merging per-sample VCF files before submission. This allows the data to be easily reusable/reproducible.

• Population allele frequencies: Alleles typically exist at different frequencies in different populations and this information provides useful supporting evidence for all submitted variants. Population-level allele frequencies can be provided in the INFO field of the VCF (see section 1.6.1 of the VCF specification).
• Individual genotypes: EVA accepts individual genotypes from samples provided by donors that have consented to having their DNA sequence housed in a public database. Genotypes can be provided in the FORMAT field of the VCF (see section 1.6.2 of the VCF specification).

The EVA requires that all variants are submitted with an asserted position on an INSDC sequence. This means that the reference allele submitted for every variant must match the position in a sequence that has been accessioned in either GenBank or ENA database. An “INSDC sequence” can be any of, but not restricted to, the following assembled sequences:

• Genome assembly
• Transcriptome
• Gene sequence

Aligning all of our submitted data with INSDC sequences enables integration with other EMBL-EBI resources including Ensembl and is an important step in maintaining standardisation at the EVA. Importantly this requires all sequence identifiers in your VCF to match those in the reference FASTA file.

The basic template of a minimal VCF file, where no genotypes are given, looks like this:

                                                ##fileformat=VCFv4.3
                                                #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
                                            

We advise submitters to consult the VCF specification (specifically sections 1.1 and 5) when converting data to VCF in order to ensure that files generated are valid, as this is a mandatory requirement.

Conversion of spreadsheet to VCF

Representing variant data in a spreadsheet can be convenient when you have a small number of variants to report. This file can be used as an example or template: spreadsheet_to_vcf.xlsx (you will need to create a copy). When reporting a large number of variants, the use of specialised software may be a better approach.

Using a spreadsheet editor, you can use the 'Save as' feature to convert the given file to a tab delimited text file. This can also be done using an online editor such as Google Sheets with the 'Download as' option. A tab character will be applied between values entered into separate cells. The result should be a file named 'spreadsheet_to_vcf.tsv'.

The file can be renamed as appropriate although the extension must be changed from '.tsv' to '.vcf' to create a VCF file.

The data entered will remain the same, and the file can be manually checked to ensure spaces between entries are tabulated and there are no extra spaces at the end of lines.

Conversion from PED / genotyping array files to VCF

You can use PLINK1.9 to convert from PLINK text format to VCF, using the command --recode vcf, along with --reference-allele to select the reference alleles. Find more details here.

Useful tools for handling VCF files

• VCF Validation: EVA VCF validation suite
• Sorting, merging and manipulation of VCF files: bcftools
• Variant callers: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict

Examples of valid VCF submissions

• PRJEB27443 - Simple INDEL submission with allele frequencies
• PRJEB27177 - Single sample VCF with genotype
• PRJEB27093 - Multiple sample VCF with genotypes
• PRJEB4163 - VCF with population allele frequencies and genotypes
• PRJEB6041 - VCF with allele counts (for calculating AF)

Further examples can be found on our FTP site.

Submission validation processes

The EVA VCF validation suite provides tools to check file validity previous to submission.

VCF Specification:

All VCF files submitted to EVA are validated for adherence to the format standard using the EVA VCF validation suite which includes all the checks from the vcftools suite, and some more that involve lexical, syntactic and semantic analysis of the VCF input. The EVA VCF validation suite also includes a debugging tool to automatically correct many of the common errors found in files. To improve processing time, submitters are encouraged to pre-validate VCF files prior to submission.

Genome Assembly:

To improve interoperability of variant data submitted to EVA with other resources at EMBL-EBI, and the wider open-access community, all submitted VCF files are subject to validation against the INSDC accessioned reference sequence indicated by the submitter in their metadata. The EVA VCF validation suite provides an assembly checker tool to validate the reference alleles in the VCF files against the reference sequence. EVA is able to only accept files that match a known sequence at 100%.

Archive process

All VCF files and novel samples that are submitted to EVA are permanently and securely archived at the European Nucleotide Archive and BioSamples, respectively. The EVA provides access to all submitted data via the Study Browser.

Variants within VCF files submitted to EVA are normalised, annotated and used for statistical calculations (via methodologies described below) and these EVA processed data are available via the Study Browser, Variant Browser and the REST API.

Finally, the EVA brokers all submitted data to the NCBI: dbSNP, for short variants (<50bp) dbVar for large variants (>50bp)

Yes. EVA, like dbSNP, accepts submission of genetic variation data that is described in Variant Call Format (VCF) files. However, unlike dbSNP, EVA does not have a custom VCF specification. Instead EVA only accepts submission of VCF files that conform to the specification guidelines. Conformity to these guidelines is checked at time of submission, but can also be checked beforehand using the EVA VCF validation suite. Further guidelines for submission to EVA can be found here.

No. Although there are many similarities, the EVA and dbSNP metadata templates, which are submitted along with VCF files, are different. The EVA metadata template asks the submitter to provide information about the project and samples so that these can be archived simultaneously along with the VCF file(s), whereas this is a stepwise process during dbSNP submission. The EVA metadata template can be found here and a mocked up version for a fictional study is here. Detailed information on how to submit to the EVA can be found here.

Yes. Data submitted to the EVA can be held privately for up to two years. The date of publication is set by the submitter using the "Hold Date" field of the EVA metadata template.

Archived data can be referenced using the project accession & associated URL e.g. The variant data for this study have been deposited in the European Variation Archive (EVA) at EMBL-EBI under accession number PRJEBxxxx (https://www.ebi.ac.uk/eva/?eva-study=PRJEB*****)

The EVA can be cited directly using the associated literature:

Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S, Flicek P, Parkinson H, Keane TM. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 2021 Oct 28:gkab960. doi: 10.1093/nar/gkab960. PMID: 34718739.