[ensembl-dev] VEP annotate VCF with protein sequence

Will McLaren wm2 at ebi.ac.uk
Mon Dec 19 09:28:00 GMT 2016


There isn't currently an implementation for this, no - it should be fairly
easy to modify ProteinSeqs to do as you wish though. Please do let us know
if you need any guidance with that.


Will McLaren

On 16 December 2016 at 15:15, Irsan Kooi <irsankooi88 at gmail.com> wrote:

> ( tried to post this message to the developers mailing list before but I
> cannot find it in the archives so I am unsure whether it arrived or not, so
> excuse me in case I already posted this question.)
> The VEP plugin called ProteinSeqs outputs the full length reference and
> mutant protein sequence of missense nonsynonymous variants. I would like to
> get substrings of protein sequences, for example 10 amino acids upstream
> and downstream of mutation and add them as columns in the VCF. Should I
> adopt the current ProteinSeqs module to my needs or is there already an
> implementation of which I am not aware of?
> Many thanks in advance!
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