[ensembl-dev] VEP using CADD plugin

[Will McLaren]

Hello,

Correct, the plugin was intended to work with the whole_genome_SNVs.tsv
file, which only contains data for SNVs.

I've modified the plugin so that it should be able to cope with indel data
files such as you have; please do let me know if you have any problems as
I've only sparingly tested it on made-up data!

Regards

Will McLaren
Ensembl Variation


On 7 May 2014 15:37, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> There seem to be a discrepancy between the CADD score calculated using VEP
> with the CADD.pm plugin and the tabix direct output:
>
> For example using this 1000G variant:
>
> #CHROM POS ID REF ALT QUAL FILTER INFO
> 7 86214932 rs140931361 TTACTC T . PASS .
>
> variant_effect_predictor.pl -i input.txt --format vcf --plugin
> CADD,/media/sf_D_DRIVE/Projects/Databases/CADD/v1.0/1000G.tsv.gz
> does not return any CADD score
>
> whereas
> $ tabix -p vcf 1000G.tsv.gz 7:86214932-86214932
> 7 86214932 TTACTC T -0.420243 2.040
>
> This seems to affect indels and not SNVs. I could see in the plugin that
> there is a rule to ignore indels. Any suggestions please how to safely
> change that?
>
> Also, in the plugin, I assume there is a test to ensure the alleles are
> identical between the input file and the 1000G.tsv.gz file. Is this correct?
>
> Thanks.
>
> --
> G.
>
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