[ensembl-dev] VEP CADD

Will McLaren wm2 at ebi.ac.uk
Mon Feb 22 09:45:46 GMT 2016

Hi Eva,

Yes, if you add the --no_consequences flag then it will skip consequence
prediction. Due to the internal mechanics of the VEP though it has to
assign the default consequence type, so everything will come out as
"intergenic_variant". Apologies, it seems this flag is missing from the

You could also restrict the output fields to just those from CADD using
e.g. "--fields CADD_RAW,CADD_PHRED".

Also note that if using VCF output, by default VEP will overwrite any
existing CSQ keys in your VCFs info field; you can add --keep_csq to avoid
this, or --vcf_info_field to have it write the data to a different key.



Will McLaren
Ensembl Variation

On 19 February 2016 at 17:05, Eva Goncalves Serra <egs at sanger.ac.uk> wrote:

> Hi,
> How can I use VEP to solely add CADD scores that I have in a file, using a
> plugin, and for not to perform anything else like consequence prediction,
> etc. Any help?
> Cheers,
> Eva
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