[ensembl-dev] VEP CADD

[Eva Goncalves Serra]

Thanks a lot Will!

Cheers,
Eva


From: <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org>> on behalf of Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Monday, 22 February 2016 09:45
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] VEP CADD

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 documentation.

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.

http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html

Regards

Will McLaren
Ensembl Variation

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