The Variant Recoder, available on the Ensembl REST API, can help you with data re-use. Multiple identifiers, coming from different databases, can refer to the same variant – the Variant Recoder can help.
You can input variants in a variety of formats to return variant identifiers, as well as HGVS descriptions, in a reproducible, easy-to-use JSON format. The Variant Recoder accepts descriptions from the Human Genome Variation Society (HGVS), genomic SPDI notations, and identifiers from databases (such as dbSNP, ClinVar and UniProt).
In release 103, we will update Variant Recoder to return allele-specific results. This will evaluate each allele separately, and present each as a single object. For multi-allelic sites, this should make the output much clearer to follow.
In this example, there are two alternative alleles, T and C. Each allele is shown as one object in the list, each with its own set of key-value pairs:
This is much clearer to follow than the existing version, shown below, where there is a single object for the variant, but a list of values for each of the keys, including all possible alleles:
Finally, we are happy to announce that a new web interface will be available for Variant Recoder in our coming release. You will be able to upload files or paste variant identifiers in the input text box, and select the output formats. Results will be displayed in a table with links to relevant Ensembl displays and external resources, and can be downloaded in JSON, a simple tab-delimited or VCF format.