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<p>Hi Margaret,</p>
<p>You obtain SNV in the CADD_RAW column, because you have using the
file : whole_genome_SNVs_inclAnno.tsv.gz instead of :
whole_genome_SNVs.tsv.gz that contains CADD score.<br>
</p>
<p>CADD plugin only reports scores and does not consider any
additional annotations from a CADD file. It is therefore
sufficient to use CADD files without the additional annotations. <br>
</p>
<p>Hope this helps</p>
<p>Best regards</p>
<p>Souhila<br>
</p>
<div class="moz-cite-prefix">Le 07/04/2020 à 22:55, Linan, Margaret
a écrit :<br>
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<p class="MsoNormal">Hi –<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am trying to use vep in tab delimited
mode. But no matter what I do, I keep seeing SNV in the
CADD_RAW column.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><u>Here is my command</u></b>:<o:p></o:p></p>
<p class="MsoNormal">./vep -i ./project_data/top200k.vcf --tab
--assembly GRCh38 --cache --offline --dir_plugins
/root/.vep/Plugins --plugin
CADD,./project_data/whole_genome_SNVs_in<o:p></o:p></p>
<p class="MsoNormal">clAnno.tsv.gz,./project_data/InDels_inclAnno.tsv.gz
-o annotations.vcf --everything --variant_class --sift b
--polyphen b --ccds --uniprot --hgvs --symbol --num<o:p></o:p></p>
<p class="MsoNormal">bers --domains --regulatory --canonical
--protein --biotype --uniprot --tsl --appris --gene_phenotype
--af --af_1kg --af_esp --af_gnomad --max_af --pubmed --var<o:p></o:p></p>
<p class="MsoNormal">iant_class –mane<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Margaret<o:p></o:p></p>
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