[ensembl-dev] VEP using CADD plugin

[Genomeo Dev]

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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