[ensembl-dev] CADD_RAW is SNV

[Thomas Danhorn]

I noticed that all of the variants in your spreadsheet have "intergenic" 
in the Consequence column, and that most (all?) of the columns with 
missing data pertain to genes or proteins, which are not applicable for 
intergenic variants, so I would expect them to be empty.

Hope this helps,

Thomas


On Wed, 8 Apr 2020, Linan, Margaret wrote:

> Hi Souhila,
>
>
> Thanks, that worked. But there is still missing data for the other columns, what can I do to fix this? Please see my attached annotated file.
>
> 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.tsv.gz,./project_data/InDels.tsv.gz -o annotations.vcf --everything --variant_class --sift b --polyphen b --ccds --uniprot --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_esp --af_gnomad --max_af --pubmed --variant_class -mane
>
> Best,
> Margaret
>
>
> From: Souhila Amanzougarene <souhila.amanzougarene at cnrs.fr>
> Sent: Wednesday, April 8, 2020 12:46 AM
> To: Ensembl developers list <dev at ensembl.org>; Linan, Margaret <margaret.linan at mssm.edu>
> Subject: Re: [ensembl-dev] CADD_RAW is SNV
>
> USE CAUTION: External Message.
>
>
> 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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