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

danny.kunz at gmx.de danny.kunz at gmx.de
Fri Feb 12 05:29:12 GMT 2021

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?




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