[ensembl-dev] differences in vep field types

[William McLaren]

Hi Michael,

Any fields that can have multiple values should be returned as a list, not a comma-separated string, so I’d say this is a bug in the  old code which has not been comprehensively fixed in the new.

Can you please provide a complete list of those fields you’ve found a problem with? We’ll then get these fixed for release/91.

Regards

Will McLaren
Ensembl Variation


On 1 November 2017 at 12:56:13 pm, D'Eletto, Michael (michael.d'eletto at ynhh.org) wrote:

Hi Ensembl team,

I've been using VEP for the past year (release 83) and I'm trying to test / validate the latest VEP version (release 90).  We use the "--json" flag as the method of output, but noticed that the field types changed between release 83 and release 90.  Is this due to changes in the new "vep" script versus the "variant_effect_predictor.pl" script?  Specifically, some fields like "pubmed" and "clin_sig" were converted from arrays / lists to concatenated strings in the latest version, and other fields like "trembl" and "swissprot" were converted from concatenated strings to arrays / lists.  Just curious if this was intentional or a bug.  For example:

"pubmed": [20632448, 21356067]

vs

"pubmed": "20632448,21356067"

Thank you,

Mike D'Eletto



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