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<div>Thanks a lot Will! </div>
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<div>Cheers,</div>
<div>Eva</div>
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<span style="font-weight:bold">From: </span><<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>> on behalf of Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Monday, 22 February 2016 09:45<br>
<span style="font-weight:bold">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] VEP CADD<br>
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<div dir="ltr">Hi Eva,
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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.</div>
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<div>You could also restrict the output fields to just those from CADD using e.g. "--fields CADD_RAW,CADD_PHRED".</div>
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<div>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.</div>
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<div><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html</a><br>
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<div>Regards</div>
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<div>Will McLaren</div>
<div>Ensembl Variation</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On 19 February 2016 at 17:05, Eva Goncalves Serra <span dir="ltr">
<<a href="mailto:egs@sanger.ac.uk" target="_blank">egs@sanger.ac.uk</a>></span> wrote:<br>
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<div>Hi,</div>
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<div>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?</div>
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<div>Cheers,</div>
<div>Eva</div>
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