[ensembl-dev] JSON output missing data

Andrew Parton aparton at ebi.ac.uk
Fri Feb 26 09:46:38 GMT 2021


Hi Michael,

If you add the —symbol flag to your VEP command then this should provide the gene symbol info with your JSON output.

If there’s anything else we can do to help, please let us know.

Kind Regards,
Andrew

> On 25 Feb 2021, at 19:33, Rightmire, Michael Paul <m.rightmire at dkfz-heidelberg.de> wrote:
> 
> Hello, 
> 
> I'm using the VEP command line from the Docker container with both JSON and VCF output. I've noticed that the JSON output is missing fields that are shown in the VCF file. 
> 
> For example, the CSQ (from the INFO column in the VCF file) contains the gene's SYMBOL. The JSON output does not (not for any of the variants.) Both the JSON and the VCF output is from the same original VCF input file. 
> 
> The sample JSON found at https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#json <https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#json> does show a "gene_symbol" key, which is missing from my output. 
> 
> The commands used to generate the two annotation outputs were...​
> vep  --cache  --dir_cache=/opt/vep/.vep  -i  "/path/$filename"  -o  "/path/${filename}.annotated.vcf"  --offline  --vcf  --force_overwrite
> 
> vep  --cache  --dir_cache=/opt/vep/.vep  -i  "/path/$filename"  -o  "/path/${filename}.annotated.json"  --offline  --json  --force_overwrite
> 
> Should I be using additional switches to get the comparable output?
> 
> Thanks!
> Mike
> 
> Michael Rightmire
> Bioinformatics and Omics Data Analytics (B240)
> Omics Software Architect
> 
> German Cancer Research Center (DKFZ)
> Im Neuenheimer Feld 280
> 69120 Heidelberg
> Germany
> phone: +49 176 7131 8758
> fax: +49 6221 42-3563
> 
> M.Rightmire at dkfz-heidelberg.de <mailto:m.mustermann at dkfz.de>
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