[ensembl-dev] FTP + variation rs id synonym mappings

Andrew Parton aparton at ebi.ac.uk
Thu Feb 18 18:08:19 GMT 2021

Hi Danny,

Currently, we do not have a file contains all of these mappings. However, VEP will allow you to annotate your VCFs with the variation synonym data that we have, by providing known synonyms for colocated variants: https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_var_synonyms <https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_var_synonyms>

Additionally, it may be possible for us to generate these synonyms in a single file as part of our next release, however VEP should be a quicker solution for you.

Kind Regards,

> On 12 Feb 2021, at 05:29, danny.kunz at gmx.de wrote:
> Hi all,
> Quick question:
> Our pipeline has to deal with VCF from older assembly releases from the GRCH37 branch.
> We tried utilizing the FTP variation VCF files, but realized that we only have hits in about 40% of the patient VCF ids matched within the FTP variation data.
> Obviously the old rs ids (synonyms) from the older assemblies are not contained in those newer releases.
> Is there any file on the FTP which contains those synonym mappings?
> -
> Calling the REST api does not cause a problem with the old rs ids as it translates them to the newer ones, but if we want to reduce the REST communication overhead, it would be helpful to be able to achieve the same with the FTP data, right?
> Thanks,
> Danny
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