[ensembl-dev] VEP annotate VCF with protein sequence

Irsan Kooi irsankooi88 at gmail.com
Fri Dec 16 15:15:57 GMT 2016

( 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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