[ensembl-dev] JSON output missing data

Rightmire, Michael Paul m.rightmire at dkfz-heidelberg.de
Thu Feb 25 19:33:45 GMT 2021


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 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?



Michael Rightmire

Bioinformatics and Omics Data Analytics (B240)

Omics Software Architect

German Cancer Research Center (DKFZ)

Im Neuenheimer Feld 280

69120 Heidelberg


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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