[ensembl-dev] CADD_RAW is SNV

Linan, Margaret margaret.linan at mssm.edu
Wed Apr 8 18:06:33 BST 2020

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


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

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



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