[ensembl-dev] [VEP] Bug stripping REF/ALT alleles ?

[William McLaren]

Hi João,

VEP trims alleles if the substitution is unbalanced (typically an insertion or deletion where the length(REF) != length(ALT)), and by default only trims the first base from each.

You may force VEP to fully strip each pair of alleles using --minimal [1]; using this flag I get missense as expected.

We’re currently working on expanding and clarifying the documentation for this, with the update available in release 90.

Regards

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_minimal

On 14 July 2017 at 11:03:40, João Eiras (joao.eiras at gmail.com) wrote:

Hi.  

I stumbled upon COSMIC annotation COSM366465  
http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=366465  

The annotations is in the VCF as  

chr4 46977409 COSM366465 CCT CAT  

VEP annotates this as (splice_region_variant,coding_sequence_variant)  
over transcript ENST00000264318. This transcript is in the reverse tr  

However, this is actually a SNP in the last nucleotide.  

The variant can be stripped as  

chr4 46977410 COSM366465 C A  

and in this case VEP does annotate it as a missense_variant.  

Without looking at the code, my guess is that VEP strips the common  
nucleotides of he tips of REF and ALT from the left in case of a  
forward strand transcript, and right side in case of a backward strand  
transcript. So, the left most C remains there and VEP thinks that  
nucleotide is changed.  

Am I missing something ?  
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