[ensembl-dev] VEP annotate VCF with protein sequence

[Irsan Kooi]

OK thanks, Yes the ProteinSeqs.pm module is an excellent starting point.

On Mon, Dec 19, 2016 at 10:28 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hello,
>
> 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.
>
> Regards
>
> 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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>
>
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