[ensembl-dev] invalid vcf output

[Reece Hart]

Hi-

VEP 72 reports protein consequences that contain an equal sign in the CSQ
INFO section. This violates the VCF spec, which says "INFO additional
information: (String, no white-space, semi-colons, or equals-signs
permitted;" (http://goo.gl/R0C1U)

Example:
variant_effect_predictor.pl  --database --vcf -o - --hgvs

with the variant ENST00000341065.4:c.1163G>C

returns a record that contains
 ... ENST00000341065.4:c.1163G>C|ENST00000341065.4:c.1163G>C(p.=)| ...

I don't know whether there is an escaping mechanism for the INFO sections,
so I'm not sure what should be done about this.

Thanks,
Reece
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