[ensembl-dev] CADD_RAW is SNV

[Souhila Amanzougarene]

Hi Margaret,

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.

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.

Hope this helps

Best regards

Souhila

Le 07/04/2020 à 22:55, Linan, Margaret a écrit :
>
> Hi –
>
> 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.
>
> *_Here is my command_*:
>
> ./vep -i ./project_data/top200k.vcf --tab --assembly GRCh38 --cache 
> --offline --dir_plugins /root/.vep/Plugins --plugin 
> CADD,./project_data/whole_genome_SNVs_in
>
> clAnno.tsv.gz,./project_data/InDels_inclAnno.tsv.gz -o annotations.vcf 
> --everything --variant_class --sift b --polyphen b --ccds --uniprot 
> --hgvs --symbol --num
>
> bers --domains --regulatory --canonical --protein --biotype --uniprot 
> --tsl --appris --gene_phenotype --af --af_1kg --af_esp --af_gnomad 
> --max_af --pubmed --var
>
> iant_class –mane
>
> Best,
>
> Margaret
>
>
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