[ensembl-dev] Synonymous HGVSp

Will McLaren wm2 at ebi.ac.uk
Fri Oct 31 09:18:52 GMT 2014

Hi Konrad,

This is done so that particular HGVS notation doesn't break parsers working
on the INFO field of VCF files (which have key1=value;key2=value2 etc).

You can switch this off if you like with --no_escape


Will McLaren
Ensembl Variation

On 31 October 2014 05:12, Konrad Karczewski <konradk at broadinstitute.org>

> Hi dev team,
> When outputting to VCF with --everything (implying --hgvs), the HGVS
> output for synonymous variants is p.%3D (i.e. the HTML code for equals is
> being printed out in the VCF) - is this supposed to be "p.="?
> Thanks!
> -Konrad
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