[ensembl-dev] differences in vep field types

[William McLaren]

Hi Mike,

Thanks, that confirms what I’ve found checking through the code.

You’re correct in that VEP doesn’t control what comes back from plugins.

Thanks for the feedback

Will


On 3 November 2017 at 8:44:39 am, D'Eletto, Michael (michael.d'eletto at ynhh.org) wrote:

Hi Will,

It looks like its only the "clin_sig" and "pubmed" fields.  There are a few other fields I see in the output, but those are coming from the dbNSFP plugin, so I'm not sure if VEP controls the output format for fields added by plugins.  For default VEP without plugins, only the "clin_sig" and "pubmed" fields seem to be affected.

Best,

Mike D'Eletto


On 11/02/2017 09:37 AM, William McLaren wrote:
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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